annotate bismark_bowtie2_wrapper.xml @ 2:82814a8a2395 draft

added samtools 0.1.19 as dependency
author bgruening
date Wed, 21 Aug 2013 05:19:54 -0400
parents 62c6da72dd4a
children 91f07ff056ca
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82814a8a2395 added samtools 0.1.19 as dependency
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1 <tool id="bismark_bowtie2" name="Bismark" version="0.7.12.1">
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2 <!-- Wrapper compatible with Bismark version 0.7.11 -->
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3 <description>bisulfite mapper (bowtie2)</description>
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4 <!--<version_command>bismark version</version_command>-->
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5 <requirements>
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6 <requirement type="set_environment">SCRIPT_PATH</requirement>
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82814a8a2395 added samtools 0.1.19 as dependency
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7 <requirement type="package" version="0.1.19">samtools</requirement>
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8 <requirement type="package" version="2.1.0">bowtie2</requirement>
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9 </requirements>
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10 <parallelism method="basic"></parallelism>
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11 <command interpreter="python">
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12 bismark_wrapper.py
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13
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14 ## Change this to accommodate the number of threads you have available.
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15 --num-threads 24
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16
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17 --bismark_path \$SCRIPT_PATH
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18
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19 --bowtie2
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20
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21 ##
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22 ## Bismark Genome Preparation, if desired.
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23 ##
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24
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25 ## Handle reference file.
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26 #if $refGenomeSource.genomeSource == "history":
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27 --own-file=$refGenomeSource.ownFile
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28 #else:
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29 --indexes-path ${refGenomeSource.index.fields.path}
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30 #end if
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31
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32
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33 ##
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34 ## Input parameters
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35 ##
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36
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37
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38 #if $singlePaired.sPaired == "single":
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39 --single-paired $singlePaired.input_singles
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40
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41 #if $singlePaired.input_singles.ext == "fastqillumina":
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42 --phred64-quals
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43 --fastq
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44 #elif $singlePaired.input_singles.ext == "fastqsanger":
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45 --fastq
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46 #elif $singlePaired.input_singles.ext == "fasta":
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47 --fasta
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48 #end if
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49 #else:
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50 --mate-paired
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51 #set $mate1 = list()
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52 #set $mate2 = list()
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53 #for $mate_pair in $singlePaired.mate_list
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54 $mate1.append( str($mate_pair.input_mate1) )
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55 $mate2.append( str($mate_pair.input_mate2) )
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56 #end for
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57
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58 --mate1 #echo ','.join($mate1)
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59 --mate2 #echo ','.join($mate2)
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60
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61 #if $singlePaired.mate_list[0].input_mate1.ext == "fastqillumina":
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62 --phred64-quals
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63 --fastq
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64 #elif $singlePaired.mate_list[0].input_mate1.ext == "fastqsanger":
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65 --fastq
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66 #elif $singlePaired.mate_list[0].input_mate1.ext == "fasta":
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67 --fasta
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68 #end if
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69
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70 -I $singlePaired.minInsert
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71 -X $singlePaired.maxInsert
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72 #end if
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73
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74
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75 ## for now hardcode the value for the required memory per thread in --best mode
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76 --chunkmbs 512
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77
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78
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79 #if $params.settingsType == "custom":
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80
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81 ## default 20
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82 --seed-len $params.seed_len
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83 ## default 0
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84 --seed-mismatches $params.seed_mismatches
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85 ## default 15
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86 --seed-extention-attempts $params.seed_extention_attempts
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87 ## default 2
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88 --max-reseed $params.max_reseed
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89
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90 ## default 70
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91 ##--maqerr $params.maqerr
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92
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93 ## default unlimited
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94 #if $params.qupto != 0:
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95 --qupto $params.qupto
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96 #end if
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97 #if $params.skip_reads != 0:
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98 --skip-reads $params.skip_reads
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99 #end if
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100
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101 ## if set, disable the original behaviour
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102 $params.no_mixed
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103 ## if set, disable the original behaviour
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104 $params.no_discordant
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105
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106 #if $params.bismark_stdout:
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107 --stdout $output_stdout
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108 #end if
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109
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110 #if $params.isReportOutput:
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111 --output-report-file $report_file
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112 #end if
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113
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114 #end if
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115
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116 ##
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117 ## Output parameters.
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118 ##
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119 --output $output
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120 ##$suppress_header
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121
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122 #if str( $singlePaired.sPaired ) == "single"
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123 #if $output_unmapped_reads_l
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124 --output-unmapped-reads $output_unmapped_reads_l
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125 #end if
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126 #if $output_suppressed_reads_l
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127 --output-suppressed-reads $output_suppressed_reads_l
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128 #end if
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129 #else
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130 #if $output_unmapped_reads_l and $output_unmapped_reads_r
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131 --output-unmapped-reads-l $output_unmapped_reads_l
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132 --output-unmapped-reads-r $output_unmapped_reads_r
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133 #end if
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134 #if $output_suppressed_reads_l and $output_suppressed_reads_l
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135 --output-suppressed-reads-l $output_suppressed_reads_l
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136 --output-suppressed-reads-r $output_suppressed_reads_r
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137 #end if
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138 #end if
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139
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140 </command>
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141 <inputs>
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142 <conditional name="refGenomeSource">
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143 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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144 <option value="indexed">Use a built-in index</option>
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145 <option value="history">Use one from the history</option>
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146 </param>
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147 <when value="indexed">
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148 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
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149 <options from_data_table="bowtie2_indexes">
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150 <filter type="sort_by" column="2"/>
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151 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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152 </options>
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153 </param>
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154 </when> <!-- build-in -->
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155 <when value="history">
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156 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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157 </when> <!-- history -->
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158 </conditional> <!-- refGenomeSource -->
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159
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160 <!-- Input Parameters -->
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161 <conditional name="singlePaired">
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162 <param name="sPaired" type="select" label="Is this library mate-paired?">
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163 <option value="single">Single-end</option>
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164 <option value="paired">Paired-end</option>
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165 </param>
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166 <when value="single">
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167 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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168 </when>
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169 <when value="paired">
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170 <repeat name="mate_list" title="Paired End Pairs" min="1">
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171 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 1" help="FASTQ or FASTA files." />
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172 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Mate pair 2" help="FASTQ or FASTA files." />
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173 </repeat>
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174 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
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175 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
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176 </when>
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177 </conditional>
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178
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179
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180 <conditional name="params">
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181 <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
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182 <option value="default">Use Defaults</option>
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183 <option value="custom">Full parameter list</option>
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184 </param>
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185 <when value="default" />
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186 <!-- Full/advanced params. -->
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187 <when value="custom">
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188 <!-- -N -->
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189 <param name="seed_mismatches" type="integer" value="0" label="Number of mismatches to be allowed in a seed alignment during multiseed alignment" />
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190 <!-- -L -->
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191 <param name="seed_len" type="integer" value="20" label="Length of the seed substrings to align during multiseed alignment" />
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192 <!--
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193 <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." />
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194 -->
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195 <!-- -D -->
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196 <param name="seed_extention_attempts" type="integer" value="15" label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on" />
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197 <!-- -R -->
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198 <param name="max_reseed" type="integer" value="2" label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds" />
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199
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200 <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." />
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201 <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" />
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202
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203 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="false" label="Disable looking for discordant alignments if it cannot find any concordant alignments" help="" />
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204 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="false" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates" help="" />
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205
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206 <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write ambiguous reads to an extra output file" help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." />
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207 <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write all reads that could not be aligned to a file" />
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208 <!-- output Options -->
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209 <param name="bismark_stdout" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write the bismark output and summary information to an extra file" />
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210 <param name="isReportOutput" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Offer all report files concatenated in one file" />
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211
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212 <!--end output options -->
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213 </when> <!-- full -->
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214 </conditional> <!-- params -->
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215 <!--
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216 <param name="suppress_header" type="boolean" truevalue="..suppress-header" falsevalue="" checked="false" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default." />
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217 -->
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218 </inputs>
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219
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220
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221 <outputs>
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222 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: Report">
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223 <filter>
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224 ((
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225 params['settingsType'] == "custom" and
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226 params['isReportOutput'] is True
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227 ))
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228 </filter>
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229 </data>
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230 <data format="txt" name="output_stdout" label="${tool.name} on ${on_string}: Summary">
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231 <filter>
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232 ((
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233 params['settingsType'] == "custom" and
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234 params['bismark_stdout'] is True
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235 ))
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236 </filter>
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237 </data>
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238
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239 <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
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240 <actions>
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241 <conditional name="refGenomeSource.genomeSource">
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242 <when value="indexed">
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243 <action type="metadata" name="dbkey">
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244 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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245 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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246 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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247 </option>
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248 </action>
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249 </when>
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250 <when value="history">
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251 <action type="metadata" name="dbkey">
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252 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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253 </action>
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254 </when>
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255 </conditional>
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256 </actions>
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257 </data>
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258
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259 <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
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260 <filter>
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261 ((
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262 params['settingsType'] == "custom" and
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263 params['suppressed_read_file'] is True
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264 ))
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265 </filter>
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266 <actions>
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267 <conditional name="singlePaired.sPaired">
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268 <when value="single">
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269 <action type="format">
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270 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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271 </action>
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272 </when>
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273 <when value="paired">
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274 <action type="format">
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275 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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276 </action>
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277 </when>
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278 </conditional>
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279 </actions>
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280 </data>
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281
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282 <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
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283 <filter>singlePaired['sPaired'] == "paired"</filter>
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284 <filter>params['settingsType'] == "custom"</filter>
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285 <filter>params['supressed_read_file'] is True</filter>
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286 <actions>
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287 <conditional name="singlePaired.sPaired">
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288 <when value="single">
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289 <action type="format">
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290 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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291 </action>
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292 </when>
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293 <when value="paired">
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294 <action type="format">
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295 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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296 </action>
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297 </when>
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298 </conditional>
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299 </actions>
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300 </data>
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301
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302 <!-- Outout unmapped reads -->
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303 <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
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304 <filter>
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305 ((
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306 params['settingsType'] == "custom" and
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307 params['unmapped_read_file'] is True
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308 ))
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309 </filter>
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310 <actions>
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311 <conditional name="singlePaired.sPaired">
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312 <when value="single">
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313 <action type="format">
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314 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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315 </action>
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316 </when>
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317 <when value="paired">
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318 <action type="format">
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319 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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320 </action>
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321 </when>
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322 </conditional>
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323 </actions>
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324 </data>
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325
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326 <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
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327 <filter>singlePaired['sPaired'] == "paired"</filter>
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328 <filter>params['settingsType'] == "custom"</filter>
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329 <filter>params['unmapped_read_file'] is True</filter>
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330 <actions>
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331 <conditional name="singlePaired.sPaired">
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332 <when value="single">
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333 <action type="format">
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334 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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335 </action>
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336 </when>
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337 <when value="paired">
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338 <action type="format">
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339 <option type="from_param" name="singlePaired.mate_list[0].input_mate1" param_attribute="ext" />
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340 </action>
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341 </when>
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342 </conditional>
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343 </actions>
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344 </data>
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345
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346
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347 </outputs>
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348
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349 <tests>
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350 </tests>
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351
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parents:
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352 <help>
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353
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parents:
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354 **What it does**
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355
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356 Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
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parents:
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357 reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
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358 version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
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359 Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
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360 (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
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361 forward strand, by doing this alignments will produce the same positions). These instances of Bowtie 2
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362 are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
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363 sequence from the genome and determine if there were any protected C's present or not.
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364
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parents:
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365 .. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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366
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367 As of version 0.7.0 Bismark will only run 2 alignment threads for OT and OB in parallel, the 4 strand mode can be
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368 re-enabled by using non_directional mode.
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369
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370 It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.
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parents:
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371
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parents:
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372 ------
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373
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parents:
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374 **Know what you are doing**
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parents:
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375
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parents:
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376 .. class:: warningmark
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377
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parents:
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378 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
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379
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380 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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381
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382
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parents:
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383 .. class:: warningmark
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384
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parents:
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385 Make sure all your input reads are in the correct and same format. If thats not the case please adjust/convert the filetype with galaxy's build-in converters.
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parents:
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386
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parents:
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387 ------
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parents:
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388
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parents:
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389 **Input formats**
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parents:
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390
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parents:
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391 Bismark accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*), Illumina FASTQ format (galaxy type *fastqillumina*) or FASTA format (galaxy type *fasta*). Use the FASTQ Groomer to prepare your files.
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parents:
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392
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parents:
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393 ------
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parents:
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394
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parents:
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395 **A Note on Built-in Reference Genomes**
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396
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parents:
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397 The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
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parents:
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398
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parents:
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399 ------
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400
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401 The final output of Bismark is in SAM format by default.
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parents:
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402
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parents:
diff changeset
403 **Outputs**
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parents:
diff changeset
404
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parents:
diff changeset
405 The output is in SAM format, and has the following columns::
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parents:
diff changeset
406
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parents:
diff changeset
407 Column Description
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parents:
diff changeset
408 -------- --------------------------------------------------------
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parents:
diff changeset
409 1 QNAME seq-ID
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parents:
diff changeset
410 2 FLAG this flag tries to take the strand a bisulfite read
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parents:
diff changeset
411 originated from into account
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parents:
diff changeset
412 (this is different from ordinary DNA alignment flags!)
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parents:
diff changeset
413 3 RNAME chromosome
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parents:
diff changeset
414 4 POS start position
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parents:
diff changeset
415 5 MAPQ always 255
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parents:
diff changeset
416 6 CIGAR extended CIGAR string
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parents:
diff changeset
417 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
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parents:
diff changeset
418 8 MPOS 1-based Mate POSition
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parents:
diff changeset
419 9 ISIZE Inferred insert SIZE
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parents:
diff changeset
420 10 SEQ query SEQuence on the same strand as the reference
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parents:
diff changeset
421 11 QUAL Phred33 scale
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parents:
diff changeset
422 12 NM-tag edit distance to the reference)
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parents:
diff changeset
423 13 XX-tag base-by-base mismatches to the reference.
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parents:
diff changeset
424 This does not include indels.
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parents:
diff changeset
425 14 XM-tag methylation call string
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parents:
diff changeset
426 15 XR-tag read conversion state for the alignment
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parents:
diff changeset
427 16 XG-tag genome conversion state for the alignment
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parents:
diff changeset
428
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parents:
diff changeset
429
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parents:
diff changeset
430 Each read of paired-end alignments is written out in a separate line in the above format.
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parents:
diff changeset
431
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parents:
diff changeset
432
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parents:
diff changeset
433 It looks like this (scroll sideways to see the entire example)::
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parents:
diff changeset
434
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parents:
diff changeset
435 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
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parents:
diff changeset
436 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
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parents:
diff changeset
437 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
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parents:
diff changeset
438
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parents:
diff changeset
439 -------
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parents:
diff changeset
440
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parents:
diff changeset
441 **Bismark settings**
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parents:
diff changeset
442
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parents:
diff changeset
443 All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.
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parents:
diff changeset
444
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parents:
diff changeset
445 ------
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parents:
diff changeset
446
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parents:
diff changeset
447 **Bismark parameter list**
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parents:
diff changeset
448
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parents:
diff changeset
449 This is an exhaustive list of Bismark options.
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parents:
diff changeset
450
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parents:
diff changeset
451 Input::
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parents:
diff changeset
452
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parents:
diff changeset
453 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g.
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parents:
diff changeset
454 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
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parents:
diff changeset
455 produce one mapping result and one report file per input file.
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parents:
diff changeset
456
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parents:
diff changeset
457 -1 mates1 Comma-separated list of files containing the #1 mates (filename usually includes
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parents:
diff changeset
458 "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
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parents:
diff changeset
459 correspond file-for-file and read-for-read with those specified in mates2.
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parents:
diff changeset
460 Reads may be a mix of different lengths. Bismark will produce one mapping result
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parents:
diff changeset
461 and one report file per paired-end input file pair.
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parents:
diff changeset
462
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parents:
diff changeset
463 -2 mates2 Comma-separated list of files containing the #2 mates (filename usually includes
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parents:
diff changeset
464 "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
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parents:
diff changeset
465 correspond file-for-file and read-for-read with those specified in mates1.
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parents:
diff changeset
466 Reads may be a mix of different lengths.
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parents:
diff changeset
467
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parents:
diff changeset
468 -q/--fastq The query input files (specified as mate1,mate2 or singles are FASTQ
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parents:
diff changeset
469 files (usually having extension .fg or .fastq). This is the default. See also
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parents:
diff changeset
470 --solexa-quals.
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parents:
diff changeset
471
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parents:
diff changeset
472 -f/--fasta The query input files (specified as mate1,mate2 or singles are FASTA
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parents:
diff changeset
473 files (usually havin extension .fa, .mfa, .fna or similar). All quality values
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parents:
diff changeset
474 are assumed to be 40 on the Phred scale.
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parents:
diff changeset
475
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parents:
diff changeset
476 -s/--skip INT Skip (i.e. do not align) the first INT reads or read pairs from the input.
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parents:
diff changeset
477
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parents:
diff changeset
478 -u/--upto INT Only aligns the first INT reads or read pairs from the input. Default: no limit.
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parents:
diff changeset
479
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parents:
diff changeset
480 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
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parents:
diff changeset
481
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parents:
diff changeset
482 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
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parents:
diff changeset
483
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parents:
diff changeset
484 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
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parents:
diff changeset
485 (which can't). The formula for conversion is:
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parents:
diff changeset
486 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
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parents:
diff changeset
487 is usually the right option for use with (unconverted) reads emitted by the GA
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parents:
diff changeset
488 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
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parents:
diff changeset
489
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parents:
diff changeset
490 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted)
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parents:
diff changeset
491 reads emitted by GA Pipeline version 1.3 or later. Default: off.
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parents:
diff changeset
492
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parents:
diff changeset
493
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parents:
diff changeset
494 Alignment::
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parents:
diff changeset
495
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parents:
diff changeset
496 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
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parents:
diff changeset
497 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the
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parents:
diff changeset
498 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
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parents:
diff changeset
499
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parents:
diff changeset
500 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to
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parents:
diff changeset
501 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
62c6da72dd4a Uploaded
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parents:
diff changeset
502 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
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parents:
diff changeset
503
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parents:
diff changeset
504 -e/--maqerr INT Maximum permitted total of quality values at all mismatched read positions throughout
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parents:
diff changeset
505 the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
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parents:
diff changeset
506 quality values to the nearest 10 and saturates at 30. This value is not relevant for
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parents:
diff changeset
507 Bowtie 2.
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parents:
diff changeset
508
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parents:
diff changeset
509 --chunkmbs INT The number of megabytes of memory a given thread is given to store path descriptors in
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parents:
diff changeset
510 --best mode. Best-first search must keep track of many paths at once to ensure it is
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parents:
diff changeset
511 always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
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parents:
diff changeset
512 memory impact of the descriptors, but they can still grow very large in some cases. If
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parents:
diff changeset
513 you receive an error message saying that chunk memory has been exhausted in --best mode,
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parents:
diff changeset
514 try adjusting this parameter up to dedicate more memory to the descriptors. This value
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parents:
diff changeset
515 is not relevant for Bowtie 2. Default: 512.
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parents:
diff changeset
516
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parents:
diff changeset
517 -I/--minins INT The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
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parents:
diff changeset
518 a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
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parents:
diff changeset
519 with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
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parents:
diff changeset
520 satisfied). A 19-bp gap would not be valid in that case. Default: 0.
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parents:
diff changeset
521
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parents:
diff changeset
522 -X/--maxins INT The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
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parents:
diff changeset
523 a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
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parents:
diff changeset
524 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
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parents:
diff changeset
525 A 61-bp gap would not be valid in that case. Default: 500.
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parents:
diff changeset
526
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parents:
diff changeset
527
62c6da72dd4a Uploaded
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parents:
diff changeset
528
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parents:
diff changeset
529 Output::
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parents:
diff changeset
530
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parents:
diff changeset
531 --non_directional The sequencing library was constructed in a non strand-specific manner, alignments to all four
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parents:
diff changeset
532 bisulfite strands will be reported. Default: OFF.
62c6da72dd4a Uploaded
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parents:
diff changeset
533
62c6da72dd4a Uploaded
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parents:
diff changeset
534 (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
62c6da72dd4a Uploaded
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parents:
diff changeset
535 to the original strands are merely theoretical and should not exist in reality. Specifying directional
62c6da72dd4a Uploaded
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parents:
diff changeset
536 alignments (which is the default) will only run 2 alignment threads to the original top (OT)
62c6da72dd4a Uploaded
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parents:
diff changeset
537 or bottom (OB) strands in parallel and report these alignments. This is the recommended option
62c6da72dd4a Uploaded
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parents:
diff changeset
538 for sprand-specific libraries).
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parents:
diff changeset
539
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parents:
diff changeset
540 --sam-no-hd Suppress SAM header lines (starting with @). This might be useful when very large input files are
62c6da72dd4a Uploaded
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parents:
diff changeset
541 split up into several smaller files to run concurrently and the output files are to be merged.
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parents:
diff changeset
542
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parents:
diff changeset
543 --quiet Print nothing besides alignments.
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parents:
diff changeset
544
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parents:
diff changeset
545 --vanilla Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
62c6da72dd4a Uploaded
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parents:
diff changeset
546 of SAM format output.
62c6da72dd4a Uploaded
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parents:
diff changeset
547
62c6da72dd4a Uploaded
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parents:
diff changeset
548 -un/--unmapped Write all reads that could not be aligned to a file in the output directory. Written reads will
62c6da72dd4a Uploaded
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parents:
diff changeset
549 appear as they did in the input, without any translation of quality values that may have
62c6da72dd4a Uploaded
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parents:
diff changeset
550 taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
62c6da72dd4a Uploaded
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parents:
diff changeset
551 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
62c6da72dd4a Uploaded
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parents:
diff changeset
552 with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
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parents:
diff changeset
553 are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
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parents:
diff changeset
554
62c6da72dd4a Uploaded
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parents:
diff changeset
555 --ambiguous Write all reads which produce more than one valid alignment with the same number of lowest
62c6da72dd4a Uploaded
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parents:
diff changeset
556 mismatches or other reads that fail to align uniquely to a file in the output directory.
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parents:
diff changeset
557 Written reads will appear as they did in the input, without any of the translation of quality
62c6da72dd4a Uploaded
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parents:
diff changeset
558 values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
62c6da72dd4a Uploaded
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parents:
diff changeset
559 parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
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parents:
diff changeset
560 _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
62c6da72dd4a Uploaded
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parents:
diff changeset
561
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parents:
diff changeset
562 -o/--output_dir DIR Write all output files into this directory. By default the output files will be written into
62c6da72dd4a Uploaded
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parents:
diff changeset
563 the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
62c6da72dd4a Uploaded
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parents:
diff changeset
564 to create it first. The path to the output folder can be either relative or absolute.
62c6da72dd4a Uploaded
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parents:
diff changeset
565
62c6da72dd4a Uploaded
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parents:
diff changeset
566 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If
62c6da72dd4a Uploaded
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parents:
diff changeset
567 the specified folder does not exist, Bismark will attempt to create it first. The path to the
62c6da72dd4a Uploaded
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parents:
diff changeset
568 temporary folder can be either relative or absolute.
62c6da72dd4a Uploaded
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parents:
diff changeset
569
62c6da72dd4a Uploaded
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parents:
diff changeset
570 ------
62c6da72dd4a Uploaded
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parents:
diff changeset
571
62c6da72dd4a Uploaded
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parents:
diff changeset
572 Bowtie 2 alignment options::
62c6da72dd4a Uploaded
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parents:
diff changeset
573
62c6da72dd4a Uploaded
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parents:
diff changeset
574 -N INT Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
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parents:
diff changeset
575 Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
62c6da72dd4a Uploaded
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parents:
diff changeset
576 but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
62c6da72dd4a Uploaded
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parents:
diff changeset
577 Bowtie 1 see -n).
62c6da72dd4a Uploaded
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parents:
diff changeset
578
62c6da72dd4a Uploaded
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parents:
diff changeset
579 -L INT Sets the length of the seed substrings to align during multiseed alignment. Smaller values
62c6da72dd4a Uploaded
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parents:
diff changeset
580 make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
62c6da72dd4a Uploaded
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parents:
diff changeset
581 used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
62c6da72dd4a Uploaded
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parents:
diff changeset
582 Bowtie 1 see -l).
62c6da72dd4a Uploaded
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parents:
diff changeset
583
62c6da72dd4a Uploaded
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parents:
diff changeset
584 --ignore-quals When calculating a mismatch penalty, always consider the quality value at the mismatched
62c6da72dd4a Uploaded
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parents:
diff changeset
585 position to be the highest possible, regardless of the actual value. I.e. input is treated
62c6da72dd4a Uploaded
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parents:
diff changeset
586 as though all quality values are high. This is also the default behavior when the input
62c6da72dd4a Uploaded
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parents:
diff changeset
587 doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
62c6da72dd4a Uploaded
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parents:
diff changeset
588
62c6da72dd4a Uploaded
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parents:
diff changeset
589
62c6da72dd4a Uploaded
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parents:
diff changeset
590 Bowtie 2 paired-end options::
62c6da72dd4a Uploaded
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parents:
diff changeset
591
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parents:
diff changeset
592 --no-mixed This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
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593 it cannot find a concordant or discordant alignment for a pair. This option is invariable and
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594 and on by default.
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595
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596 --no-discordant Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
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597 A discordant alignment is an alignment where both mates align uniquely, but that does not
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598 satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
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599 and it is on by default.
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600
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601
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602 Bowtie 2 effort options::
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603
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604 -D INT Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
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parents:
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605 the alignments found so far. A seed extension "fails" if it does not yield a new best or a
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606 new second-best alignment. Default: 15.
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607
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608 -R INT INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
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609 When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
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parents:
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610 mismatches allowed) at different offsets and searches for more alignments. A read is considered
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611 to have repetitive seeds if the total number of seed hits divided by the number of seeds
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612 that aligned at least once is greater than 300. Default: 2.
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613
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614
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615 Bowtie 2 Scoring options::
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parents:
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616
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617 --score_min "func" Sets a function governing the minimum alignment score needed for an alignment to be considered
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parents:
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618 "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
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619 L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
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620 See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
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621 L,0,-0.2.
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622
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623
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624 Bowtie 2 Reporting options::
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625
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parents:
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626 --most_valid_alignments INT This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is
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627 deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
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parents:
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628 default mode, but adjusting the -M setting is deprecated. Use the -D and -R options to adjust the
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parents:
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629 effort expended to find valid alignments.
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630
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631 For reference, this used to be the old (now deprecated) description of -M:
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parents:
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632 Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
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633 can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
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634 happens first. Only the best alignment is reported. Information from the other alignments is used to
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635 estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes
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636 Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
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637 aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
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638 guarantee that the alignment reported is the best possible in terms of alignment score. -M is
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639 always used and its default value is set to 10.
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640
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641 </help>
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642 </tool>