annotate rsem_calculate_expression.xml @ 5:14267d364365 default tip

Update for dataset files_path - use model from BB pull request 532
author Jim Johnson <jj@umn.edu>
date Thu, 04 Feb 2016 06:50:26 -0600
parents 30a8343fb0e7
children
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1 <tool id="rsem_calculate_expression" name="RSEM calculate expression" version="1.1.17">
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2 <description>RNA-Seq by Expectation-Maximization</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.17">rsem</requirement>
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5 <requirement type="package" version="1.0.0">bowtie</requirement>
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6 </requirements>
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7 <command>
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8 rsem-calculate-expression
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9 ## --tag string
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10 #if $seedlength:
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11 --seed-length $seedlength
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12 #end if
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13 --forward-prob $forward_prob
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14 #if $rsem_options.fullparams == 'fullset':
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15 ## Fragment info
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16 #if $rsem_options.fragment_length_mean:
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17 --fragment-length-mean $rsem_options.fragment_length_mean
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18 #end if
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19 #if $rsem_options.fragment_length_min:
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20 --fragment-length-min $rsem_options.fragment_length_min
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21 #end if
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22 #if $rsem_options.fragment_length_sd:
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23 --fragment-length-sd $rsem_options.fragment_length_sd
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24 #end if
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25 #if $rsem_options.fragment_length_max:
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26 --fragment-length-max $rsem_options.fragment_length_max
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27 #end if
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28 ## RSPD
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29 #if $rsem_options.rspd.estimate == 'yes':
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30 --estimate-rspd
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31 #if $rsem_options.rspd.num_rspd_bins:
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32 --num-rspd-bins $rsem_options.rspd.num_rspd_bins
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33 #end if
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34 #end if
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35 ## Calculate 95% credibility intervals and posterior mean estimates.
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36 #if $rsem_options.useci.ci == 'yes':
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37 --calc-ci
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38 #if $rsem_options.useci.cimem:
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39 --ci-memory $rsem_options.useci.cimem
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40 #end if
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41 #end if
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42 #end if
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43 ## --num-threads $GALAXY_SLOTS
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44 #if $input.format != 'bam' and $input.bowtie_options.fullparams == 'fullset':
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45 ## Bowtie params
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46 #if $bowtie_options.bowtie_e:
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47 --bowtie-e $bowtie_options.bowtie_e
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48 #end if
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49 #if $bowtie_options.bowtie_m:
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50 --bowtie-m $bowtie_options.bowtie_m
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51 #end if
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52 #if $bowtie_options.bowtie_n:
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53 --bowtie-n $bowtie_options.bowtie_n
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54 #end if
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55 #end if
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56 ## Outputs
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57 #if $rsem_outputs.result_bams == 'none':
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58 --no-bam-output
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59 #else
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60 #if $rsem_outputs.result_bams == 'both':
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61 --output-genome-bam
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62 #end if
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63 $rsem_outputs.sampling_for_bam
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64 #end if
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65 ## Input data
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66 #if $input.format=="fastq"
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67 $input.fastq_select
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68 #if $input.fastq.matepair=="single":
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69 $input.fastq.singlefastq
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70 #elif $input.fastq.matepair=="paired":
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71 --paired-end
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72 $input.fastq.fastq1
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73 $input.fastq.fastq2
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74 #end if
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75 #elif $input.format=="fasta"
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76 --no-qualities
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77 #if $input.fasta.matepair=="single":
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78 $input.fasta.singlefasta
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79 #elif $input.fasta.matepair=="paired":
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80 --paired-end
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81 $input.fasta.fasta1
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82 $input.fasta.fasta2
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83 #end if
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84 #elif $input.format=="sam"
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85 #if $input.matepair=="paired":
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86 --paired-end
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87 #end if
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88 #if $input.rsem_sam._extension == 'sam':
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89 --sam
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90 #elif $input.rsem_sam._extension == 'bam':
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91 --bam
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92 #end if
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93 $input.rsem_sam
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94 #end if
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95 ## RSEM reference
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96 #if $reference.refSrc == 'history':
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97 ${reference.rsem_ref.extra_files_path}/${reference.rsem_ref.metadata.reference_name}
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98 #elif $reference.refSrc == 'cached':
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99 ${reference.index.fields.path}
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100 #end if
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101 ## sample_name: use a hard coded name so we can pull out galaxy outputs
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102 rsem_output
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103 ## direct output into logfile
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104 > $log
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105 </command>
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106 <macros>
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107 <macro name="rsem_options">
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108 <param name="seedlength" type="integer" value="25" optional="true" label="Seed length used by the read aligner" help="Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. RSEM uses this value for Bowtie's seed length parameter. The minimum value is 25. (Default:25)">
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109 </param>
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110 <param name="forward_prob" type="select" label="Is the library strand specific?">
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111 <option value="0.5" selected="true">No</option>
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112 <option value="1">Yes, the reads (or first reads from paired-end libraries) are only in the forward orientation</option>
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113 <option value="0">Yes, the reads (or first reads from paired-end libraries) are only in the reverse orientation</option>
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114 </param>
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115 <conditional name="rsem_options">
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116 <param name="fullparams" type="select" label="Additional RSEM options">
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117 <option value="default">Use RSEM Defaults</option>
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118 <option value="fullset">Set Additional RSEM Options</option>
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119 </param>
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120 <when value="default"/>
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121 <when value="fullset">
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122 <param name="fragment_length_min" type="integer" value="1" optional="true" label="Minimum read/insert length." help=" This is also the value for the bowtie -I option">
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123 <validator type="in_range" message="0 or greater" min="0" />
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124 </param>
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125 <param name="fragment_length_max" type="integer" value="1000" optional="true" label="Maximum read/insert length." help=" This is also the value for the bowtie -X option">
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126 <validator type="in_range" message="0 or greater" min="0" max="1000000"/>
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127 </param>
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128 <param name="fragment_length_mean" type="float" value="" optional="true" label="Fragment length mean (single-end data only)" help="The mean of the fragment length distribution, which is assumed to be a Gaussian. (Default: -1, which disables use of the fragment length distribution)">
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129 </param>
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130 <param name="fragment_length_sd" type="float" value="" optional="true" label="The standard deviation of the fragment length distribution (single-end data only)" help="Default 0, which assumes that all fragments are of the same length, given by the rounded value of fragment length mean. ">
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131 </param>
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132 <conditional name="rspd">
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133 <param name="estimate" type="select" lanel="Read Start Position Distribution (RSPD)"
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134 help="Set this option if you want to estimate the read start position distribution (RSPD) from data. Otherwise, RSEM will use a uniform RSPD.">
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135 <option value="no" selected="true">Use a uniform RSPD</option>
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136 <option value="yes">Estimate and correct for a non-uniform RSPD</option>
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137 </param>
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138 <when value="no"/>
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139 <when value="yes">
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140 <param name="num_rspd_bins" type="integer" value="20" optional="true" label="Number of bins in the RSPD." help="Use of the default setting of 20 is recommended.">
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141 <validator type="in_range" message="" min="0" max="100"/>
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142 </param>
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143 </when>
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144 </conditional>
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145 <conditional name="useci">
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146 <param name="ci" type="select" label="Calculate 95% Credibility Intervals">
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147 <option value="no" selected="true">no</option>
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148 <option value="yes">yes</option>
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149 </param>
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150 <when value="no"/>
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151 <when value="yes">
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152 <param name="cimem" size="4" type="text" value="1024" label="Amount of memory in (MB) for computing CI" />
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153 </when>
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154 </conditional>
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155 </when>
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156 </conditional>
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157 </macro>
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158 <macro name="bowtie_options">
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159 <conditional name="bowtie_options">
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160 <param name="fullparams" type="select" label="bowtie settings">
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161 <option value="default">use bowtie defaults</option>
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162 <option value="fullset">set bowtie options</option>
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163 </param>
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164 <when value="default"/>
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165 <when value="fullset">
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166 <param name="bowtie_n" type="integer" value="2" optional="true" label="Bowtie mismatches" help="Bowtie parameter max # of mismatches in the seed. (Range: 0-3, Default: 2) ">
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167 <validator type="in_range" message="max # of mismatches in the seed between 0 and 3" min="0" max="3"/>
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168 </param>
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169 <param name="bowtie_e" type="integer" value="99999999" label="Maximum sum of quality scores at mismatched positions in read alignments. This is also the value for the Bowtie -e option">
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170 </param>
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171 <param name="bowtie_m" type="integer" value="200" label="Discard alignments for reads with number of alignments greater than">
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172 </param>
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173 </when>
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174 </conditional>
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175 </macro>
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176 <macro name="sampling_for_bam">
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177 <param name="sampling_for_bam" type="boolean" truevalue="--sampling-for-bam" falsevalue="" checked="false" label="Use sampling for BAM">
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178 <help> When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
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179 </help>
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180 </param>
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181 </macro>
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182 </macros>
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183
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184 <inputs>
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185 <param name="sample" type="text" value="rsem_sample" label="Sample name" />
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186 <conditional name="reference">
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187 <param name="refSrc" type="select" label="RSEM Reference Source">
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188 <option value="cached">Locally cached</option>
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189 <option value="history">From your history</option>
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190 </param>
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191 <when value="cached">
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192 <param name="index" type="select" label="Select RSEM reference" help="Select from a list of pre-indexed references. If you don't see anything consult the wrapper's documentation on how to create or download a reference">
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193 <options from_data_table="rsem_indexes">
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194 <filter type="sort_by" column="2" />
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195 <validator type="no_options" message="No indexes are available" />
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196 </options>
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197 </param>
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198 </when>
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199 <when value="history">
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200 <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" />
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jjohnson
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201 </when>
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jjohnson
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diff changeset
202 </conditional>
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jjohnson
parents:
diff changeset
203 <conditional name="input">
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jjohnson
parents:
diff changeset
204 <param name="format" type="select" label="RSEM Input file type">
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jjohnson
parents:
diff changeset
205 <option value="fastq">FASTQ</option>
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jjohnson
parents:
diff changeset
206 <option value="fasta">FASTA</option>
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jjohnson
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diff changeset
207 <option value="sam">SAM/BAM</option>
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jjohnson
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208 </param>
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jjohnson
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diff changeset
209 <when value="fastq">
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jjohnson
parents:
diff changeset
210 <param name="fastq_select" size="15" type="select" label="FASTQ type" >
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jjohnson
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211 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
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jjohnson
parents:
diff changeset
212 <option value="--solexa-quals">solexa qualities</option>
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jjohnson
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diff changeset
213 <option value="--phred64-quals">phred64 qualities</option>
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jjohnson
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214 </param>
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jjohnson
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diff changeset
215 <conditional name="fastq">
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jjohnson
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216 <param name="matepair" type="select" label="Library type">
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jjohnson
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217 <option value="single">Single End Reads</option>
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jjohnson
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218 <option value="paired">Paired End Reads</option>
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jjohnson
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219 </param>
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jjohnson
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220 <when value="single">
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jjohnson
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221 <param name="singlefastq" type="data" format="fastq" label="FASTQ file" />
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jjohnson
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222 </when>
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jjohnson
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diff changeset
223 <when value="paired">
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jjohnson
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224 <param name="fastq1" type="data" format="fastq" label="Read 1 fastq file" />
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jjohnson
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225 <param name="fastq2" type="data" format="fastq" label="Read 2 fastq file" />
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jjohnson
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226 </when>
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jjohnson
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227 </conditional>
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jjohnson
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diff changeset
228 <expand macro="bowtie_options"/>
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jjohnson
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229 </when>
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jjohnson
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diff changeset
230 <when value="fasta">
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jjohnson
parents:
diff changeset
231 <conditional name="fasta">
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jjohnson
parents:
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232 <param name="matepair" type="select" label="Library Type">
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jjohnson
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233 <option value="single">Single End Reads</option>
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jjohnson
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234 <option value="paired">Paired End Reads</option>
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jjohnson
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235 </param>
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jjohnson
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diff changeset
236 <when value="single">
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jjohnson
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237 <param name="singlefasta" type="data" format="fasta" label="fasta file" />
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jjohnson
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238 </when>
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jjohnson
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diff changeset
239 <when value="paired">
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jjohnson
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240 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
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jjohnson
parents:
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241 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
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jjohnson
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242 </when>
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jjohnson
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243 </conditional>
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jjohnson
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diff changeset
244 <expand macro="bowtie_options"/>
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jjohnson
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245 </when>
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jjohnson
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246 <when value="sam">
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jjohnson
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247 <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam -->
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jjohnson
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diff changeset
248 <param name="matepair" type="select" label="Library Type">
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jjohnson
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249 <option value="single">Single End Reads</option>
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jjohnson
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diff changeset
250 <option value="paired">Paired End Reads</option>
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jjohnson
parents:
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251 </param>
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jjohnson
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252 <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" />
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jjohnson
parents:
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253 </when>
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jjohnson
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254 </conditional>
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jjohnson
parents:
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255 <expand macro="rsem_options"/>
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jjohnson
parents:
diff changeset
256 <conditional name="rsem_outputs">
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jjohnson
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257 <param name="result_bams" type="select" label="Create bam results files"
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jjohnson
parents:
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258 help="In addition to the transcript-coordinate-based BAM file output, also output a BAM file with the read alignments in genomic coordinates" >
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jjohnson
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259 <option value="none">No BAM results files</option>
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jjohnson
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260 <option value="default" selected="true">Transcript BAM results file</option>
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jjohnson
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261 <option value="both">Transcript and genome BAM results files</option>
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jjohnson
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262 </param>
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jjohnson
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diff changeset
263 <when value="none"/>
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jjohnson
parents:
diff changeset
264 <when value="default">
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jjohnson
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diff changeset
265 <expand macro="sampling_for_bam"/>
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jjohnson
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266 </when>
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jjohnson
parents:
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267 <when value="both">
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jjohnson
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268 <expand macro="sampling_for_bam"/>
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jjohnson
parents:
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269 </when>
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jjohnson
parents:
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270 </conditional>
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jjohnson
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271 </inputs>
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jjohnson
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272 <stdio>
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jjohnson
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273 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
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jjohnson
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274 </stdio>
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jjohnson
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275 <outputs>
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jjohnson
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276 <data format="tabular" name="gene_abundances" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/>
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jjohnson
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277 <data format="tabular" name="isoform_abundances" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/>
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jjohnson
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278 <data format="bam" name="transcript_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.bam" >
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jjohnson
parents:
diff changeset
279 <filter>rsem_outputs['result_bams'] != "none"</filter>
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jjohnson
parents:
diff changeset
280 </data>
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jjohnson
parents:
diff changeset
281 <data format="bam" name="transcript_sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
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jjohnson
parents:
diff changeset
282 <filter>rsem_outputs['result_bams'] != "none"</filter>
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jjohnson
parents:
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283 </data>
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jjohnson
parents:
diff changeset
284 <data format="bam" name="genome_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.bam">
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jjohnson
parents:
diff changeset
285 <filter>rsem_outputs['result_bams'] == "both"</filter>
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jjohnson
parents:
diff changeset
286 </data>
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jjohnson
parents:
diff changeset
287 <data format="bam" name="genome_sorted_bam" label="${sample}.genome.sorted.bam" from_work_dir="rsem_output.genome.sorted.bam">
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jjohnson
parents:
diff changeset
288 <filter>rsem_outputs['result_bams'] == "both"</filter>
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jjohnson
parents:
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289 </data>
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jjohnson
parents:
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290 <data format="txt" name="log" label="${sample}.rsem_log"/>
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jjohnson
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291 </outputs>
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jjohnson
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diff changeset
292 <tests>
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jjohnson
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diff changeset
293 <test>
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jjohnson
parents:
diff changeset
294 <param name="sample" value="rsem_sample"/>
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jjohnson
parents:
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295 <param name="refSrc" value="history"/>
2
5949673f9e3e rename test data RSEM_ref_reference.rsem_ref
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
296 <param name="rsem_ref" value="RSEM_ref_reference.rsem_ref" ftype="rsem_ref"/>
0
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jjohnson
parents:
diff changeset
297 <param name="format" value="fastq"/>
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jjohnson
parents:
diff changeset
298 <param name="matepair" value="single"/>
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jjohnson
parents:
diff changeset
299 <param name="singlefastq" value="test.fastq" ftype="fastqsanger"/>
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jjohnson
parents:
diff changeset
300 <param name="result_bams" value="none"/>
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jjohnson
parents:
diff changeset
301 <output name="gene_abundances">
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jjohnson
parents:
diff changeset
302 <assert_contents>
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jjohnson
parents:
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303 <has_text text="ENST00000423562,ENST00000438504,ENST00000488147,ENST00000538476,ENST00000541675" />
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jjohnson
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304 </assert_contents>
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jjohnson
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305 </output>
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jjohnson
parents:
diff changeset
306 <output name="isoform_abundances">
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jjohnson
parents:
diff changeset
307 <assert_contents>
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jjohnson
parents:
diff changeset
308 <has_text text="ENST00000332831" />
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jjohnson
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309 </assert_contents>
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jjohnson
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310 </output>
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jjohnson
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311 <output name="log">
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jjohnson
parents:
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312 <assert_contents>
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jjohnson
parents:
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313 <has_text text="Expression Results are written" />
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jjohnson
parents:
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314 </assert_contents>
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jjohnson
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315 </output>
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jjohnson
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316 </test>
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jjohnson
parents:
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317 </tests>
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jjohnson
parents:
diff changeset
318 <help>
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jjohnson
parents:
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319
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jjohnson
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320
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jjohnson
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321 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
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jjohnson
parents:
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322
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jjohnson
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323 NAME
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jjohnson
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324 rsem-calculate-expression
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jjohnson
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325
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jjohnson
parents:
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326 SYNOPSIS
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jjohnson
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327 rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name
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jjohnson
parents:
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328 rsem-calculate-expression [options] --paired-end upstream_read_file/s downstream_read_file/s reference_name sample_name
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jjohnson
parents:
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329 rsem-calculate-expression [options] --sam/--bam [--paired-end] input reference_name sample_name
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jjohnson
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330
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jjohnson
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331 ARGUMENTS
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jjohnson
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332 upstream_read_files/s
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jjohnson
parents:
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333 Comma-separated list of files containing single-end reads or
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jjohnson
parents:
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334 upstream reads for paired-end data. By default, these files are
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jjohnson
parents:
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335 assumed to be in FASTQ format. If the --no-qualities option is
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jjohnson
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diff changeset
336 specified, then FASTA format is expected.
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jjohnson
parents:
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337
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jjohnson
parents:
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338 downstream_read_file/s
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jjohnson
parents:
diff changeset
339 Comma-separated list of files containing downstream reads which are
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jjohnson
parents:
diff changeset
340 paired with the upstream reads. By default, these files are assumed
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jjohnson
parents:
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341 to be in FASTQ format. If the --no-qualities option is specified,
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jjohnson
parents:
diff changeset
342 then FASTA format is expected.
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jjohnson
parents:
diff changeset
343
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jjohnson
parents:
diff changeset
344 input
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
345 SAM/BAM formatted input file. If "-" is specified for the filename,
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jjohnson
parents:
diff changeset
346 SAM/BAM input is instead assumed to come from standard input. RSEM
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jjohnson
parents:
diff changeset
347 requires all alignments of the same read group together. For
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jjohnson
parents:
diff changeset
348 paired-end reads, RSEM also requires the two mates of any alignment
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jjohnson
parents:
diff changeset
349 be adjacent. See Description section for how to make input file obey
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jjohnson
parents:
diff changeset
350 RSEM's requirements.
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jjohnson
parents:
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351
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jjohnson
parents:
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352 reference_name
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jjohnson
parents:
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353 The name of the reference used. The user must have run
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jjohnson
parents:
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354 'rsem-prepare-reference' with this reference_name before running
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jjohnson
parents:
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355 this program.
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jjohnson
parents:
diff changeset
356
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jjohnson
parents:
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357 sample_name
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jjohnson
parents:
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358 The name of the sample analyzed. All output files are prefixed by
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jjohnson
parents:
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359 this name (e.g., sample_name.genes.results)
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jjohnson
parents:
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360
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jjohnson
parents:
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361 OPTIONS
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jjohnson
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362
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jjohnson
parents:
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363 --paired-end
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jjohnson
parents:
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364 Input reads are paired-end reads. (Default: off)
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jjohnson
parents:
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365
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jjohnson
parents:
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366 --no-qualities
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jjohnson
parents:
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367 Input reads do not contain quality scores. (Default: off)
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jjohnson
parents:
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368
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jjohnson
parents:
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369 --strand-specific
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jjohnson
parents:
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370 The RNA-Seq protocol used to generate the reads is strand specific,
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jjohnson
parents:
diff changeset
371 i.e., all (upstream) reads are derived from the forward strand. This
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jjohnson
parents:
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372 option is equivalent to --forward-prob=1.0. With this option set, if
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jjohnson
parents:
diff changeset
373 RSEM runs the Bowtie aligner, the '--norc' Bowtie option will be
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jjohnson
parents:
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374 used, which disables alignment to the reverse strand of transcripts.
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jjohnson
parents:
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375 (Default: off)
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jjohnson
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376
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jjohnson
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377 --sam
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jjohnson
parents:
diff changeset
378 Input file is in SAM format. (Default: off)
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jjohnson
parents:
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379
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jjohnson
parents:
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380 --bam
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jjohnson
parents:
diff changeset
381 Input file is in BAM format. (Default: off)
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jjohnson
parents:
diff changeset
382
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jjohnson
parents:
diff changeset
383 --sam-header-info [file]
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jjohnson
parents:
diff changeset
384 RSEM reads header information from input by default. If this option
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jjohnson
parents:
diff changeset
385 is on, header information is read from the specified file. For the
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jjohnson
parents:
diff changeset
386 format of the file, please see SAM official website. (Default: "")
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jjohnson
parents:
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387
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jjohnson
parents:
diff changeset
388 -p/--num-threads [int]
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jjohnson
parents:
diff changeset
389 Number of threads to use. Both Bowtie and expression estimation will
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jjohnson
parents:
diff changeset
390 use this many threads. (Default: 1)
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jjohnson
parents:
diff changeset
391
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jjohnson
parents:
diff changeset
392 --no-bam-output
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jjohnson
parents:
diff changeset
393 Do not output any BAM file. (Default: off)
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jjohnson
parents:
diff changeset
394
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jjohnson
parents:
diff changeset
395 --output-genome-bam
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jjohnson
parents:
diff changeset
396 Generate a BAM file, 'sample_name.genome.bam', with alignments
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jjohnson
parents:
diff changeset
397 mapped to genomic coordinates and annotated with their posterior
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jjohnson
parents:
diff changeset
398 probabilities. In addition, RSEM will call samtools (included in
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jjohnson
parents:
diff changeset
399 RSEM package) to sort and index the bam file.
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jjohnson
parents:
diff changeset
400 'sample_name.genome.sorted.bam' and
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jjohnson
parents:
diff changeset
401 'sample_name.genome.sorted.bam.bai' will be generated. (Default:
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
402 off)
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jjohnson
parents:
diff changeset
403
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jjohnson
parents:
diff changeset
404 --sampling-for-bam
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jjohnson
parents:
diff changeset
405 When RSEM generates a BAM file, instead of outputing all alignments
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jjohnson
parents:
diff changeset
406 a read has with their posterior probabilities, one alignment is
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jjohnson
parents:
diff changeset
407 sampled and outputed according to the posterior probabilities. If
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jjohnson
parents:
diff changeset
408 the sampling result is that the read comes from the "noise"
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jjohnson
parents:
diff changeset
409 transcript, nothing is outputed. (Default: off)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
410
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
411 --calc-ci
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
412 Calculate 95% credibility intervals and posterior mean estimates.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
413 (Default: off)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
414
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
415 --seed-length [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
416 Seed length used by the read aligner. Providing the correct value is
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
417 important for RSEM. If RSEM runs Bowtie, it uses this value for
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
418 Bowtie's seed length parameter. Any read with its or at least one of
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
419 its mates' (for paired-end reads) length less than this value will
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
420 be ignored. If the references are not added poly(A) tails, the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
421 minimum allowed value is 5, otherwise, the minimum allowed value is
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
422 25. Note that this script will only check if the value less or equal than
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
423 5 and give a warning message if the value less than 25 but greter or equal than
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
424 5. (Default: 25)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
425
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
426 --tag [string]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
427 The name of the optional field used in the SAM input for identifying
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
428 a read with too many valid alignments. The field should have the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
429 format [tagName]:i:[value], where a [value] bigger than 0 indicates
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
430 a read with too many alignments. (Default: "")
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
431
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
432 --bowtie-path [path]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
433 The path to the bowtie executables. (Default: the path to the bowtie
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
434 executables is assumed to be in the user's PATH environment
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
435 variable)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
436
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
437 --bowtie-n [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
438 (Bowtie parameter) max # of mismatches in the seed. (Range: 0-3,
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
439 Default: 2)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
440
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
441 --bowtie-e [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
442 (Bowtie parameter) max sum of mismatch quality scores across the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
443 alignment. (Default: 99999999)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
444
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
445 --bowtie-m [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
446 (Bowtie parameter) suppress all alignments for a read if greater then [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
447 valid alignments exist. (Default: 200)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
448
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
449 --bowtie-chunkmbs [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
450 (Bowtie parameter) memory allocated for best first alignment
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
451 calculation (Default: 0 - use bowtie's default)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
452
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
453 --phred33-quals
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
454 Input quality scores are encoded as Phred+33. (Default: on)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
455
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
456 --phred64-quals
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
457 Input quality scores are encoded as Phred+64 (default for GA
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
458 Pipeline ver. less than 1.3). (Default: off)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
459
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
460 --solexa-quals
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
461 Input quality scores are solexa encoded (from GA Pipeline ver. less
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
462 than 1.3). (Default: off)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
463
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
464 --forward-prob [double]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
465 Probability of generating a read from the forward strand of a
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
466 transcript. Set to 1 for a strand-specific protocol where all
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
467 (upstream) reads are derived from the forward strand, 0 for a
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
468 strand-specific protocol where all (upstream) read are derived from
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
469 the reverse strand, or 0.5 for a non-strand-specific protocol.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
470 (Default: 0.5)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
471
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
472 --fragment-length-min [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
473 Minimum read/insert length allowed. This is also the value for the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
474 bowtie -I option. (Default: 1)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
475
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
476 --fragment-length-max [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
477 Maximum read/insert length allowed. This is also the value for the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
478 bowtie -X option. (Default: 1000)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
479
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
480 --fragment-length-mean [double]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
481 (single-end data only) The mean of the fragment length distribution,
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
482 which is assumed to be a Gaussian. (Default: -1, which disables use
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
483 of the fragment length distribution)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
484
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
485 --fragment-length-sd [double]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
486 (single-end data only) The standard deviation of the fragment length
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
487 distribution, which is assumed to be a Gaussian. (Default: 0, which
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
488 assumes that all fragments are of the same length, given by the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
489 rounded value of --fragment-length-mean)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
490
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
491 --estimate-rspd
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
492 Set this option if you want to estimate the read start position
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
493 distribution (RSPD) from data. Otherwise, RSEM will use a uniform
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
494 RSPD. (Default: off)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
495
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
496 --num-rspd-bins [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
497 Number of bins in the RSPD. Only relevant when '--estimate-rspd' is
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
498 specified. Use of the default setting is recommended. (Default: 20)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
499
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
500 --ci-memory [int]
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
501 Maximum size (in memory, MB) of the auxiliary buffer used for
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
502 computing credibility intervals (CI). Set it larger for a faster CI
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
503 calculation. However, leaving 2 GB memory free for other usage is
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
504 recommended. (Default: 1024)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
505
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
506 --keep-intermediate-files
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
507 Keep temporary files generated by RSEM. RSEM creates a temporary
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
508 directory, 'sample_name.temp', into which it puts all intermediate
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
509 output files. If this directory already exists, RSEM overwrites all
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
510 files generated by previous RSEM runs inside of it. By default,
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
511 after RSEM finishes, the temporary directory is deleted. Set this
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
512 option to prevent the deletion of this directory and the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
513 intermediate files inside of it. (Default: off)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
514
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
515 --time
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
516 Output time consumed by each step of RSEM to 'sample_name.time'.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
517 (Default: off)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
518
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
519 -q/--quiet
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
520 Suppress the output of logging information. (Default: off)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
521
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
522 -h/--help
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
523 Show help information.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
524
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
525 DESCRIPTION
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
526 In its default mode, this program aligns input reads against a reference
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
527 transcriptome with Bowtie and calculates expression values using the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
528 alignments. RSEM assumes the data are single-end reads with quality
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
529 scores, unless the '--paired-end' or '--no-qualities' options are
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
530 specified. Users may use an alternative aligner by specifying one of the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
531 --sam and --bam options, and providing an alignment file in the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
532 specified format. However, users should make sure that they align
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
533 against the indices generated by 'rsem-prepare-reference' and the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
534 alignment file satisfies the requirements mentioned in ARGUMENTS
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
535 section.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
536
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
537 One simple way to make the alignment file satisfying RSEM's requirements
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
538 (assuming the aligner used put mates in a paired-end read adjacent) is
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
539 to use 'convert-sam-for-rsem' script. This script only accept SAM format
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
540 files as input. If a BAM format file is obtained, please use samtools to
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
541 convert it to a SAM file first. For example, if '/ref/mouse_125' is the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
542 'reference_name' and the SAM file is named 'input.sam', you can run the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
543 following command:
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
544
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
545 convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
546
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
547 For details, please refer to 'convert-sam-for-rsem's documentation page.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
548
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
549 The SAM/BAM format RSEM uses is v1.4. However, it is compatible with old
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
550 SAM/BAM format. However, RSEM cannot recognize 0x100 in the FLAG field.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
551 In addition, RSEM requires SEQ and QUAL are not '*'.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
552
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
553 The user must run 'rsem-prepare-reference' with the appropriate
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
554 reference before using this program.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
555
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
556 For single-end data, it is strongly recommended that the user provide
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
557 the fragment length distribution parameters (--fragment-length-mean and
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
558 --fragment-length-sd). For paired-end data, RSEM will automatically
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
559 learn a fragment length distribution from the data.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
560
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
561 Please note that some of the default values for the Bowtie parameters
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
562 are not the same as those defined for Bowtie itself.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
563
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
564 The temporary directory and all intermediate files will be removed when
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
565 RSEM finishes unless '--keep-intermediate-files' is specified.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
566
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
567 With the '--calc-ci' option, 95% credibility intervals and posterior
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
568 mean estimates will be calculated in addition to maximum likelihood
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
569 estimates.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
570
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
571 OUTPUT
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
572 sample_name.genes.results
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
573 File containing gene level expression estimates. The format of each
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
574 line in this file is:
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
575
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
576 gene_id expected_counts tau_value [pmc_value tau_pme_value
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
577 tau_ci_lower_bound tau_ci_upper_bound] transcript_id_list
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
578
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
579 Fields are separated by the tab character. Fields within "[]" are
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
580 only presented if '--calc-ci' is set. pme stands for posterior mean
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
581 estimation. pmc stands for posterior mean counts. ci_lower_bound(l)
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
582 means the lower bound of the credibility intervals,
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
583 ci_upper_bound(u) means the upper bound of the credibility
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
584 intervals. So the credibility interval is [l, u].
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
585 'transcript_id_list' is a space-separated list of transcript_ids
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
586 belonging to the gene. If no gene information is provided, this file
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
587 has the same content as 'sample_name.isoforms.results'.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
588
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
589 sample_name.isoforms.results
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
590 File containing isoform level expression values. The format of each
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
591 line in this file is:
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
592
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
593 transcript_id expected_counts tau_value [pmc_value tau_pme_value
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
594 tau_ci_lower_bound tau_ci_upper_bound] gene_id
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
595
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
596 Fields are separated by the tab character. 'gene_id' is the gene_id
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
597 of the gene which this transcript belongs to. If no gene information
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
598 is provided, 'gene_id' and 'transcript_id' are the same.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
599
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
600 sample_name.transcript.bam, sample_name.transcript.sorted.bam and
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
601 sample_name.transcript.sorted.bam.bai
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
602 Only generated when --no-bam-output is not specified.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
603
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
604 'sample_name.transcript.bam' is a BAM-formatted file of read
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
605 alignments in transcript coordinates. The MAPQ field of each
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
606 alignment is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)),
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
607 where w is the posterior probability of that alignment being the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
608 true mapping of a read. In addition, RSEM pads a new tag ZW:f:value,
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
609 where value is a single precision floating number representing the
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
610 posterior probability.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
611
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
612 'sample_name.transcript.sorted.bam' and
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
613 'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
614 indices generated by samtools (included in RSEM package).
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
615
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
616 sample_name.genome.bam, sample_name.genome.sorted.bam and
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
617 sample_name.genome.sorted.bam.bai
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
618 Only generated when --no-bam-output is not specified and
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
619 --output-genome-bam is specified.
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
620
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
621 'sample_name.genome.bam' is a BAM-formatted file of read alignments
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
622 in genomic coordinates. Alignments of reads that have identical
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
623 genomic coordinates (i.e., alignments to different isoforms that
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
624 share the same genomic region) are collapsed into one alignment. The
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jjohnson
parents:
diff changeset
625 MAPQ field of each alignment is set to min(100, floor(-10 *
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jjohnson
parents:
diff changeset
626 log10(1.0 - w) + 0.5)), where w is the posterior probability of that
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jjohnson
parents:
diff changeset
627 alignment being the true mapping of a read. In addition, RSEM pads a
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jjohnson
parents:
diff changeset
628 new tag ZW:f:value, where value is a single precision floating
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jjohnson
parents:
diff changeset
629 number representing the posterior probability. If an alignment is
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jjohnson
parents:
diff changeset
630 spliced, a XS:A:value tag is also added, where value is either '+'
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jjohnson
parents:
diff changeset
631 or '-' indicating the strand of the transcript it aligns to.
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jjohnson
parents:
diff changeset
632
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jjohnson
parents:
diff changeset
633 'sample_name.genome.sorted.bam' and
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jjohnson
parents:
diff changeset
634 'sample_name.genome.sorted.bam.bai' are the sorted BAM file and
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jjohnson
parents:
diff changeset
635 indices generated by samtools (included in RSEM package).
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jjohnson
parents:
diff changeset
636
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jjohnson
parents:
diff changeset
637 sample_name.sam.gz
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jjohnson
parents:
diff changeset
638 Only generated when the input files are raw reads instead of SAM/BAM
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jjohnson
parents:
diff changeset
639 format files
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jjohnson
parents:
diff changeset
640
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jjohnson
parents:
diff changeset
641 It is the gzipped SAM output produced by bowtie aligner.
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jjohnson
parents:
diff changeset
642
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jjohnson
parents:
diff changeset
643 sample_name.time
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jjohnson
parents:
diff changeset
644 Only generated when --time is specified.
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jjohnson
parents:
diff changeset
645
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jjohnson
parents:
diff changeset
646 It contains time (in seconds) consumed by aligning reads, estimating
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jjohnson
parents:
diff changeset
647 expression levels and calculating credibility intervals.
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jjohnson
parents:
diff changeset
648
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jjohnson
parents:
diff changeset
649 sample_name.stat
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jjohnson
parents:
diff changeset
650 This is a folder instead of a file. All model related statistics are
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jjohnson
parents:
diff changeset
651 stored in this folder. Use 'rsem-plot-model' can generate plots
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jjohnson
parents:
diff changeset
652 using this folder.
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jjohnson
parents:
diff changeset
653
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jjohnson
parents:
diff changeset
654 EXAMPLES
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jjohnson
parents:
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655 Assume the path to the bowtie executables is in the user's PATH
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jjohnson
parents:
diff changeset
656 environment variable. Reference files are under '/ref' with name
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jjohnson
parents:
diff changeset
657 'mouse_125'.
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jjohnson
parents:
diff changeset
658
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jjohnson
parents:
diff changeset
659 1) '/data/mmliver.fq', single-end reads with quality scores. Quality
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jjohnson
parents:
diff changeset
660 scores are encoded as for 'GA pipeline version >= 1.3'. We want to use 8
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jjohnson
parents:
diff changeset
661 threads and generate a genome BAM file:
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jjohnson
parents:
diff changeset
662
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jjohnson
parents:
diff changeset
663 rsem-calculate-expression --phred64-quals \
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jjohnson
parents:
diff changeset
664 -p 8 \
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jjohnson
parents:
diff changeset
665 --output-genome-bam \
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jjohnson
parents:
diff changeset
666 /data/mmliver.fq \
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jjohnson
parents:
diff changeset
667 /ref/mouse_125 \
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jjohnson
parents:
diff changeset
668 mmliver_single_quals
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jjohnson
parents:
diff changeset
669
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
670 2) '/data/mmliver_1.fq' and '/data/mmliver_2.fq', paired-end reads with
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
671 quality scores. Quality scores are in SANGER format. We want to use 8
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
672 threads and do not generate a genome BAM file:
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jjohnson
parents:
diff changeset
673
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jjohnson
parents:
diff changeset
674 rsem-calculate-expression -p 8 \
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jjohnson
parents:
diff changeset
675 --paired-end \
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jjohnson
parents:
diff changeset
676 /data/mmliver_1.fq \
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jjohnson
parents:
diff changeset
677 /data/mmliver_2.fq \
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jjohnson
parents:
diff changeset
678 /ref/mouse_125 \
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jjohnson
parents:
diff changeset
679 mmliver_paired_end_quals
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jjohnson
parents:
diff changeset
680
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
681 3) '/data/mmliver.fa', single-end reads without quality scores. We want
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jjohnson
parents:
diff changeset
682 to use 8 threads:
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jjohnson
parents:
diff changeset
683
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jjohnson
parents:
diff changeset
684 rsem-calculate-expression -p 8 \
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jjohnson
parents:
diff changeset
685 --no-qualities \
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jjohnson
parents:
diff changeset
686 /data/mmliver.fa \
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jjohnson
parents:
diff changeset
687 /ref/mouse_125 \
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jjohnson
parents:
diff changeset
688 mmliver_single_without_quals
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jjohnson
parents:
diff changeset
689
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jjohnson
parents:
diff changeset
690 4) Data are the same as 1). We want to take a fragment length
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jjohnson
parents:
diff changeset
691 distribution into consideration. We set the fragment length mean to 150
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jjohnson
parents:
diff changeset
692 and the standard deviation to 35. In addition to a BAM file, we also
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jjohnson
parents:
diff changeset
693 want to generate credibility intervals. We allow RSEM to use 1GB of
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jjohnson
parents:
diff changeset
694 memory for CI calculation:
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jjohnson
parents:
diff changeset
695
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jjohnson
parents:
diff changeset
696 rsem-calculate-expression --bowtie-path /sw/bowtie \
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jjohnson
parents:
diff changeset
697 --phred64-quals \
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jjohnson
parents:
diff changeset
698 --fragment-length-mean 150.0 \
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jjohnson
parents:
diff changeset
699 --fragment-length-sd 35.0 \
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jjohnson
parents:
diff changeset
700 -p 8 \
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jjohnson
parents:
diff changeset
701 --output-genome-bam \
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jjohnson
parents:
diff changeset
702 --calc-ci \
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jjohnson
parents:
diff changeset
703 --ci-memory 1024 \
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jjohnson
parents:
diff changeset
704 /data/mmliver.fq \
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jjohnson
parents:
diff changeset
705 /ref/mouse_125 \
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jjohnson
parents:
diff changeset
706 mmliver_single_quals
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jjohnson
parents:
diff changeset
707
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
708 5) '/data/mmliver_paired_end_quals.bam', paired-end reads with quality
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jjohnson
parents:
diff changeset
709 scores. We want to use 8 threads:
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
710
ca988deacfd1 Uploaded
jjohnson
parents:
diff changeset
711 rsem-calculate-expression --paired-end \
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jjohnson
parents:
diff changeset
712 --bam \
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jjohnson
parents:
diff changeset
713 -p 8 \
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jjohnson
parents:
diff changeset
714 /data/mmliver_paired_end_quals.bam \
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jjohnson
parents:
diff changeset
715 /ref/mouse_125 \
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jjohnson
parents:
diff changeset
716 mmliver_paired_end_quals
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jjohnson
parents:
diff changeset
717 </help>
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jjohnson
parents:
diff changeset
718 </tool>