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1 <tool id="cuffquant" name="Cuffquant" version="@VERSION@.0">
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2 <!-- Wrapper supports Cuffdiff versions 2.2.1 -->
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3 <description>Precompute gene expression levels</description>
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4 <expand macro="requirements" />
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5 <expand macro="stdio" />
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6 <macros>
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7 <import>cuff_macros.xml</import>
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8 </macros>
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9 <version_command>cuffquant 2>&1 | head -n 1</version_command>
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10 <command>
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11 cuffquant
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12 --no-update-check
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13 --num-threads=\${GALAXY_SLOTS:-4}
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14 ## Set advanced SE data parameters?
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15 #if $additional.sAdditional == "Yes":
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16 -m $additional.frag_mean_len
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17 -s $additional.frag_len_std_dev
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18 #end if
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19
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20 ## Multi-read correct?
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21 #if $multiread_correct :
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22 -u
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23 #end if
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24
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25 ## Bias correction?
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26 #if $bias_correction.do_bias_correction == "Yes":
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27 -b
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28 #if $bias_correction.seq_source.index_source == "history":
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29 ## Custom genome from history.
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30 $bias_correction.seq_source.ref_file
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31 #else:
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32 ## Built-in genome.
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33 "${ bias_correction.seq_source.index.fields.path }"
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34 #end if
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35 #end if
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36
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37 $length_correction
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38
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39 ## Set advanced parameters for cufflinks
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40 #if $advanced_settings.sAdvanced == "Yes":
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41 #if str($advanced_settings.library_type) != 'auto':
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42 --library-type=$advanced_settings.library_type
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43 #end if
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44 #if $advanced_settings.mask_file:
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45 --mask-file=$advanced_settings.mask_file
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46 #end if
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47 --max-mle-iterations=$advanced_settings.max_mle_iterations
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48 --max-bundle-frags=$advanced_settings.max_bundle_frags
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49 #end if
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50 ## Inputs.
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51 $gtf_input
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52 #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] )
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53 $samplestring
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54 </command>
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55 <inputs>
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56 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"
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57 help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/>
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58
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59 <repeat name="samples" title="Replicate" min="1">
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60 <param name="sample" label="Add replicate" type="data" format="sam,bam"/>
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61 </repeat>
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62
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63 <param name="multiread_correct" type="boolean" label="Use multi-read correct"
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64 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." />
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65
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66 <conditional name="bias_correction">
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67 <param name="do_bias_correction" type="select" label="Perform Bias Correction"
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68 help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
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69 <option value="No">No</option>
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70 <option value="Yes">Yes</option>
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71 </param>
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72 <when value="Yes">
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73 <conditional name="seq_source">
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74 <param name="index_source" type="select" label="Reference sequence data">
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75 <option value="cached">Locally cached</option>
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76 <option value="history">History</option>
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77 </param>
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78 <when value="cached">
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79 <param name="index" type="select" label="Using reference genome">
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80 <options from_data_table="fasta_indexes">
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81 <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
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82 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
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83 </options>
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84 </param>
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85 </when>
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86 <when value="history">
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87 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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88 </when>
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89 </conditional>
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90 </when>
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91 <when value="No"></when>
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92 </conditional>
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93
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94 <param name="length_correction" type="select" label="apply length correction" help="mode of length normalization to transcript fpkm.">
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95 <option value="" selected="true">cufflinks effective length correction</option>
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96 <option value="--no-effective-length-correction">standard length correction</option>
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97 <option value="--no-length-correction">no length correction at all (use raw counts)</option>
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98 </param>
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99
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100 <conditional name="additional">
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101 <param name="sAdditional" type="select" label="Set Additional Parameters for single end reads? (not recommended for paired-end reads)">
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102 <option value="No" selected="True">No</option>
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103 <option value="Yes">Yes</option>
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104 </param>
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105 <when value="No"></when>
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106 <when value="Yes">
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107 <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/>
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108 <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/>
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109 </when>
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110 </conditional>
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111
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112 <conditional name="advanced_settings">
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113 <param name="sAdvanced" type="select" label="Set Advanced Cuffquant parameters? ">
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114 <option value="No" selected="True">No</option>
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115 <option value="Yes">Yes</option>
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116 </param>
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117 <when value="No"></when>
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118 <when value="Yes">
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119 <param type="select" name="library_type" label="Library prep used for input reads" help="">
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120 <option value="auto" selected="True">Auto Detect</option>
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121 <option value="ff-firststrand">ff-firststrand</option>
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122 <option value="ff-secondstrand">ff-secondstrand</option>
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123 <option value="ff-unstranded">ff-unstranded</option>
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124 <option value="fr-firststrand">fr-firststrand</option>
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125 <option value="fr-secondstrand">fr-secondstrand</option>
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126 <option value="fr-unstranded" >fr-unstranded</option>
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127 <option value="transfrags">transfrags</option>
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128 </param>
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129 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" />
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130 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" />
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131 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus"
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132 help="Sets the maximum number of fragments a locus may have before being skipped. Default: 500,000" />
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133 </when>
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134 </conditional>
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135 </inputs>
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136 <outputs>
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137 <!-- Standard datasets. -->
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138 <data format="cxb" name="out_file" label="${tool.name} on ${on_string}: Abundances.cxb" from_work_dir="abundances.cxb" />
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139 </outputs>
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140 <tests>
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141 <test>
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142 <!--
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143 cuffquant cuffcompare_out5.gtf cuffdiff_in1.sam,cuffdiff_in2.sam
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144 -->
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145 <param name="gtf_input" value="cuffquant_in.gtf" ftype="gtf" />
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146 <repeat name="samples">
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147 <param name="sample" value="cuffquant_in1.sam" ftype="sam" />
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148 </repeat>
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149 <repeat name="samples">
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150 <param name="sample" value="cuffquant_in2.sam" ftype="sam" />
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151 </repeat>
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152 <param name="length_correction" value="" />
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153 <param name="do_bias_correction" value="No" />
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154 <param name="multiread_correct" value="No"/>
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155 <param name="sAdditional" value="No"/>
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156 <param name="sAdvanced" value="No" />
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157 <output name="out_file" file="cuffquant_out1.cxb" compare="sim_size" />
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158 </test>
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159 </tests>
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160
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161 <help>
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162 **Cuffquant Overview**
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163
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164 Cuffquant is part of Cufflinks_. Cuffquant provides pre-calculation of gene expression levels. The resulting file can be provided to cuffdiff or cuffnorm for further processing. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
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165
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166 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
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167
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168 ------
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169
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170 **Know what you are doing**
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171
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172 .. class:: warningmark
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173
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174 There is no such thing (yet) as an automated gearshift in expression analysis. 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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175
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176 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffquant/
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177
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178 ------
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179
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180 **Input format**
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181
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182 Cuffquant takes Cufflinks or Cuffcompare GTF files as input along with two or more SAM files containing the fragment alignments for two or more samples.
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183
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184 ------
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185
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186 **Outputs**
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187
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188 Cuffquant produces one output file:
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189
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190 1. Transcript expression values in binary format.
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191
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192 -------
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193
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194 **Settings**
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195
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196 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here.
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197
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198 ------
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199
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200 **Cuffdiff parameter list**
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201
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202 This is a list of implemented Cuffdiff options::
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203
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204 -m INT Average fragment length (SE reads); default 200
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205 -s INT Fragment legnth standard deviation (SE reads); default 80
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206 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000
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207 -u Multi read correction tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.
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208 -b ref.fasta bias correction. Bias detection and correction can significantly improve accuracy of transcript abundance estimates.
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209 --no-effective-length-correction Use standard length correction
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210 --no-length-correction Disable all length correction.
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211 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
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212 --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file
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213 --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
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214 </help>
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215 <citations>
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216 <citation type="doi">10.1038/nbt.1621</citation>
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217 </citations>
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218 </tool>
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