annotate salmon.xml @ 0:91f3a2147127 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit d7607abc9feea09f0f8a227ead4da09323e167bb
author bgruening
date Tue, 15 Nov 2016 11:36:41 -0500
parents
children c1d822f84e1a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
91f3a2147127 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit d7607abc9feea09f0f8a227ead4da09323e167bb
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1 <tool id="salmon" name="Salmon" version="0.7.2">
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2
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3 <description>Transcript Quantification from RNA-seq data</description>
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4
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5 <macros>
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6 <xml name="strandedness">
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7 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
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8 <option value="U" selected="True">Not stranded (U)</option>
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9 <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
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10 <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
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11 </param>
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12 </xml>
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13 </macros>
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14
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15 <requirements>
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16 <requirement type="package" version="0.7.2">salmon</requirement>
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17 </requirements>
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18
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19 <stdio>
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20 <exit_code range="1:" />
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21 <exit_code range=":-1" />
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22 <regex match="Error:" />
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23 <regex match="Exception:" />
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24 <regex match="Exception :" />
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25 </stdio>
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26 <version_command>salmon -version</version_command>
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27 <command><![CDATA[
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28 mkdir ./index
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29 &&
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30 mkdir ./output
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31 &&
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32 #if $refTranscriptSource.TranscriptSource == "history":
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33 salmon index
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34 --transcripts $refTranscriptSource.ownFile
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35 --kmerLen $refTranscriptSource.kmerLen
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36 --threads "\${GALAXY_SLOTS:-4}"
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37 --index './index'
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38 --type '$quasi_orphans.type'
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39 $perfectHash
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40 #if str($sasamp):
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41 --sasamp $sasamp
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42 #end if
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43 #set $index_path = './index'
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44 #else:
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45 #set $index_path = $refTranscriptSource.index.fields.path
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46 #end if
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47 &&
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48 #if $single_or_paired.single_or_paired_opts == 'single':
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49 #if $single_or_paired.input_singles.ext == 'fasta':
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50 #set $ext = 'fasta'
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51 #else:
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52 #set $ext = 'fastq'
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53 #end if
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54 ln -s $single_or_paired.input_singles ./single.$ext &&
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55 #else:
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56 #if $single_or_paired.input_mate1.ext == 'fasta':
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57 #set $ext = 'fasta'
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58 #else:
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59 #set $ext = 'fastq'
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60 #end if
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61 ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
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62 ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
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63 #end if
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64 #if $geneMap:
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65 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
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66 #end if
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67 salmon quant
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68 --index $index_path
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69 #if $single_or_paired.single_or_paired_opts == 'single':
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70 --libType ${single_or_paired.strandedness}
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71 --unmatedReads ./single.$ext
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72 #else:
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73 --mates1 ./mate1.$ext
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74 --mates2 ./mate2.$ext
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75 --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
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76 #end if
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77 --output ./output
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78 #if str($quasi_orphans.type) == 'quasi':
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79 --allowOrphans
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80 #else:
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81 $quasi_orphans.allowOrphans
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82 #end if
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83 $seqBias
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84 $gcBias
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85 --threads "\${GALAXY_SLOTS:-4}"
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86 --incompatPrior $adv.incompatPrior
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87 $adv.consistentHits
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88 $adv.dumpEq
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89 #if str($adv.gcSizeSamp):
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90 --gcSizeSamp $adv.gcSizeSamp
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91 #end if
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92 #if str($adv.biasSpeedSamp):
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93 --biasSpeedSamp $adv.biasSpeedSamp
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94 #end if
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95 $adv.strictIntersect
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96 #if str($adv.fldMax):
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97 --fldMax $adv.fldMax
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98 #end if
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99 #if str($adv.fldMean):
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100 --fldMean $adv.fldMean
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101 #end if
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102 #if str($adv.fldSD):
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103 --fldSD $adv.fldSD
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104 #end if
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105 #if $adv.forgettingFactor:
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106 --forgettingFactor $adv.forgettingFactor
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107 #end if
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108 $adv.writeMappings
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109 #if str($adv.maxOcc):
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110 --maxOcc $adv.maxOcc
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111 #end if
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112 $adv.initUniform
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113 $adv.noFragLengthDist
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114 $adv.noBiasLengthThreshold
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115 #if str($adv.maxReadOcc):
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116 --maxReadOcc $adv.maxReadOcc
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117 #end if
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118 #if $geneMap:
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119 --geneMap ./geneMap.${geneMap.ext}
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120 #end if
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121 $adv.noEffectiveLengthCorrection
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122 $adv.useVBOpt
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123 #if str($adv.numBiasSamples):
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124 --numBiasSamples $adv.numBiasSamples
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125 #end if
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126 #if str($adv.numAuxModelSamples):
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127 --numAuxModelSamples $adv.numAuxModelSamples
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128 #end if
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129 #if str($adv.numPreAuxModelSamples):
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130 --numPreAuxModelSamples $adv.numPreAuxModelSamples
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131 #end if
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132 #if str($adv.numGibbsSamples):
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133 --numGibbsSamples $adv.numGibbsSamples
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134 #end if
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135 #if str($adv.numBootstraps):
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136 --numBootstraps $adv.numBootstraps
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137 #end if
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138 $adv.perTranscriptPrior
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139 #if $adv.vbPrior:
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140 --vbPrior $adv.vbPrior
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141 #end if
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142 $adv.writeUnmappedNames
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143 ]]>
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144 </command>
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145
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146 <inputs>
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147 <conditional name="refTranscriptSource">
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148 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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149 <option value="indexed">Use a built-in index</option>
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150 <option value="history" selected="True">Use one from the history</option>
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151 </param>
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152 <when value="indexed">
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153 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
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154 <options from_data_table="salmon_indexes">
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155 <filter type="sort_by" column="2"/>
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156 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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157 </options>
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158 </param>
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159 </when> <!-- build-in -->
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160 <when value="history">
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161 <param name="ownFile" type="data" format="fasta" label="Select the reference transcriptome" help="in FASTA format" />
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162 <param argument="kmerLen" type="integer" value="31" label="The size should be odd number."/>
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163 </when> <!-- history -->
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164 </conditional>
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165 <conditional name="single_or_paired">
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166 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
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167 <option value="single">Single-end</option>
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168 <option value="paired">Paired-end</option>
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169 </param>
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170 <when value="single">
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171 <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
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172 <expand macro="strandedness" />
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173 </when>
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174 <when value="paired">
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175 <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." />
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176 <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." />
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177 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
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178 <option value="M">Mates are oriented in the same direction (M = matching)</option>
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179 <option value="O">Mates are oriented away from each other (O = outward)</option>
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180 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
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181 </param>
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182 <expand macro="strandedness" />
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183 </when>
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184 </conditional>
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185 <conditional name="quasi_orphans">
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186 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
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187 <option value="quasi" selected="True">quasi</option>
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188 <option value="fmd">fmd</option>
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189 </param>
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190 <when value="quasi">
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191 </when> <!-- build-in -->
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192 <when value="fmd">
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193 <param argument="--allowOrphans" type="boolean" truevalue="--allowOrphans" falsevalue="" checked="True"
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194 label="Consider orphaned reads as valid hits when performing lightweight-alignment"
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195 help="This option will increase sensitivity (allow more reads to map and more transcripts to be detected), but may decrease specificity as orphaned alignments are more likely to be spurious."/>
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196 </when> <!-- history -->
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197 </conditional>
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198 <param argument="--perfectHash" type="boolean" truevalue="--perfectHash" falsevalue="" checked="False"
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199 label="Perfect Hash"
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200 help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification), but will take longer to construct "/>
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201 <param argument="--sasamp" type="integer" value="1" optional="True" label="Suffix Array"
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202 help="The interval at which the suffix array should be sampled. Smaller values are faster, but produce a larger index. The default should be OK, unless your transcriptome is huge. This value should be a power of 2."/>
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203 <param argument="--seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
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204 label="Perform sequence-specific bias correction"
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205 help=""/>
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206 <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
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207 label="Perform fragment GC bias correction"
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208 help=""/>
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209 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
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210 label="File containing a mapping of transcripts to genes. If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
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211 <section name="adv" title="Additional Options">
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212 <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
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213 label="Write Mappings"
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214 help=" Setting this option then the quasi-mapping results will be written out in SAM-cpmpatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead." />
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215 <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"
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216 label="Incompatible Prior"
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217 help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" />
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218 <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
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219 label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
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220 <param argument="--gcSizeSamp" type="integer" value="1" optional="True"
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221 label="The value by which to down-sample transcripts when representing the GC content" help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/>
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222 <param argument="--biasSpeedSamp" type="integer" value="1" optional="True"
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223 label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias." help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>
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224 <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False"
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225 label="Modifies how orphans are assigned." help="When this flag is set, if the intersection of the quasi-mappings for the left and right is empty, then all mappings for the left and all mappings for the right read are reported as orphaned quasi-mappings."/>
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226 <param argument="--minLen" type="integer" value="19" optional="True"
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227 label=" (S)MEMs smaller than this size won't be considered." help="" />
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228 <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="False"
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229 label="Perform sensitive quantification"
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230 help=" Setting this option enables the splitting of SMEMs that are larger than 1.5 times the minimum seed length (minLen/k above). This may reveal high scoring chains of MEMs that are masked by long SMEMs. However, this option makes lightweight-alignment a bit slower and is usually not necessary if the reference is of reasonable quality." />
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231 <param argument="--consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
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232 label="Force hits gathered during quasi-mapping to be consistent"
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233 help="" />
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234 <param argument="--extraSensitive" type="boolean" truevalue="--extraSensitive" falsevalue="" checked="False"
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235 label="Perform extra sensitive quantification"
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236 help="Setting this option enables an extra pass of 'seed' search. Enabling this option may improve sensitivity (the number of reads having sufficient coverage), but will typically slow down quantification by ~40%. Consider enabling this option if you find the mapping rate to be significantly lower than expected."/>
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237 <param argument="--coverage" type="float" value="0.69999999999999996" optional="True"
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238 label="Required coverage of read by union of SMEMs to consider it a hit"
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239 help="" />
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240 <param argument="--fldMax" type="integer" value="1000" optional="True"
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241 label="The maximum fragment length to consider when building the empirical distribution."
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242 help=""/>
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243 <param argument="--fldMean" type="integer" value="200" optional="True"
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244 label="The mean used in the fragment length distribution prior"
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245 help="If single end reads are being used for quantification, or there are an insufficient number of uniquely mapping reads when performing paired-end quantification to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/>
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246 <param argument="--fldSD" type="integer" value="80" optional="True"
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247 label="Standard deviation"
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248 help="The standard deviation used in the fragment length distribution prior."/>
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249 <param argument="--forgettingFactor" type="float" value="0.65000000000000002" optional="True"
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250 label="The forgetting factor used in the online learning schedule."
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251 help=" A smaller value results in quicker learning, but higher variance and may be unstable. A larger value results in slower learning but may be more stable. Value should be in the interval (0.5, 1.0]." />
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252 <param argument="--maxOcc" type="integer" value="200" optional="True"
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253 label="(S)MEMs occuring more than this many times won't be considered"
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254 help=""/>
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255 <param argument="--initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
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256 label="Initialization with uniform parameters"
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257 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
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258 <param argument="--maxReadOcc" type="integer" value="100" optional="True"
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259 label="Maximal read mapping occurence"
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260 help="Reads mapping to more than this many places won't be considered."/>
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261 <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
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262 label="Disable effective length correction"
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263 help="Disables effective length correction when computing the probability that a fragment was generated from a transcript. If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/>
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264 <param argument="--noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
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265 label="Ignore fragment length distribution"
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266 help="[experimental] : Don't consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location. Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment's a priori probability." />
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267 <param argument="--noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
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268 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
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269 help="This can increase the precision of bias correction, but harm robustness. The difault correction applies a threshold." />
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270 <param argument="--numBiasSamples" type="integer" value="2000000" optional="True"
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271 label="Number of fragment mappings to use when learning the sequence-specific bias model."
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272 help="" />
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273 <param argument="--numAuxModelSamples" type="integer" value="5000000" optional="True"
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274 label="The first numAuxModelSamples are used to train the auxiliary model parameters."
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275 help="(e.g. fragment length distribution, bias, etc.). After ther first numAuxModelSamples observations the auxiliary model parameters will be assumed to have converged and will be fixed." />
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276 <param argument="--numPreAuxModelSamples" type="integer" value="1000000" optional="True"
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277 label="The first numPreAuxModelSamples will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models."
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278 help=" The purpose of ignoring the auxiliary models for the first numPreAuxModelSamples observations is to avoid applying these models before thier parameters have been learned sufficiently well." />
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279 <param argument="--splitWidth" type="integer" value="0" optional="True"
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280 label=" If (S)MEM occurs fewer than this many times, search for smaller, contained MEMs"
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281 help="The default value will not split (S)MEMs, a higher value will result in more MEMs being explore and, thus, will result in increased running time." />
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282 <param argument="--splitSpanningSeeds" type="boolean" truevalue="--splitSpanningSeeds" falsevalue="" checked="False"
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283 label="Attempt to split seeds that happen to fall on the boundary between two transcripts."
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284 help="This can improve the fragment hit-rate, but is usually not necessary."/>
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285 <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
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286 label="Use the Variational Bayesian EM rather than the traditional EM algorithm for optimization in the batch passes."
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287 help=""/>
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288 <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
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289 label=" Number of Gibbs sampling rounds to perform."
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290 help="" />
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291 <param argument="--numBootstraps" type="integer" value="0" optional="True"
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292 label="Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling."
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293 help="" />
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294 <param argument="--perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="False"
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295 label="The prior will be interpreted as a transcript-level prior."
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296 help="either the default or the argument provided via --vbPrior" />
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297 <param argument="--vbPrior" type="float" value="0.001" optional="True"
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298 label="The prior that will be used in the VBEM algorithm."
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299 help="This is interpreted as a per-nucleotide prior, unless the --perTranscriptPrior flag is also given, in which case this is used as a transcript-level prior." />
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300 <param argument="--writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
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301 label="Write the names of un-mapped reads to the file unmapped_names.txt."
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302 help=""/>
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303 </section>
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304 </inputs>
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305
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306 <outputs>
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307 <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
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308 <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
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309 <filter>geneMap</filter>
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310 </data>
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311 </outputs>
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312
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313 <tests>
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314 <test>
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315 <param name="single_or_paired_opts" value="paired" />
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316 <param name="input_mate1" value="reads_1.fastq" />
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317 <param name="input_mate2" value="reads_2.fastq" />
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318 <param name="biasCorrect" value="False" />
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319 <param name="TranscriptSource" value="history" />
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320 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
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321 <output name="output_quant">
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322 <assert_contents>
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323 <has_text text="EffectiveLength" />
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324 <has_text text="TPM" />
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325 <has_text text="NM_001168316" />
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326 <has_text text="NM_174914" />
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327 <has_text text="NM_018953" />
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328 <has_text text="NR_003084" />
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329 <has_text text="NM_017410" />
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330 <has_text text="NM_153693" />
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331 <has_text text="NR_031764" />
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332 <has_n_columns n="5" />
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333 </assert_contents>
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334 </output>
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335 </test>
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336 <test>
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337 <param name="single_or_paired_opts" value="paired" />
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338 <param name="input_mate1" value="reads_1.fastq" />
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339 <param name="input_mate2" value="reads_2.fastq" />
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340 <param name="TranscriptSource" value="history" />
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341 <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
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342 <param name="geneMap" value="gene_map.tab" ftype="tabular" />
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343 <output name="output_quant">
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344 <assert_contents>
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345 <has_text text="EffectiveLength" />
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346 <has_text text="TPM" />
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347 <has_text text="NM_001168316" />
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348 <has_text text="NM_174914" />
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349 <has_text text="NM_018953" />
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350 <has_text text="NR_003084" />
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351 <has_text text="NM_017410" />
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352 <has_text text="NM_153693" />
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353 <has_text text="NR_031764" />
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354 <has_n_columns n="5" />
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355 </assert_contents>
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356 </output>
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357 <output name="output_gene_quant">
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358 <assert_contents>
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359 <has_text text="EffectiveLength" />
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360 <has_text text="TPM" />
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361 <has_text text="baz" />
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362 <has_text text="bar" />
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363 <has_text text="2283" />
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364 <has_text text="1640" />
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365 <has_n_columns n="5" />
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366 </assert_contents>
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367 </output>
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368 </test>
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369 </tests>
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370
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371 <help><![CDATA[
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372 **What it does**
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373 salmon is a tool for transcript quantification from RNA-seq data. It
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374 requires a set of target transcripts (either from a reference or de-novo
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375 assembly) to quantify. All you need to run Salmon is a fasta file containing
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376 your reference transcripts and a (set of) fasta/fastq file(s) containing your
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377 reads. Salmon runs in two phases; indexing and quantification. The indexing
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378 step is independent of the reads, and only need to be run one for a particular
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379 set of reference transcripts and choice of k (the k-mer size). The
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380 quantification step, obviously, is specific to the set of RNA-seq reads and is
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381 thus run more frequently.
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382 When the quantification output contains a number of columns:
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383 (1) Transcript ID,
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384 (2) Transcript Length,
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385 (3) Transcripts per Million (TPM) and
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386 (4) Estimated number of reads (an estimate of the number of reads drawn from this transcript given the transcript’s relative abundance and length).
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387 The first two columns are self-explanatory, the next four are measures of transcript abundance and the final is a commonly used input for differential expression tools.
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388 The Transcripts per Million quantification number is computed as described in [1], and is meant as an estimate of the number of transcripts, per million observed transcripts,
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389 originating from each isoform. Its benefit over the F/RPKM measure is that it is independent of the mean expressed transcript length
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390 (i.e. if the mean expressed transcript length varies between samples, for example, this alone can affect differential analysis based on the K/RPKM.).
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391
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392
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393 Fragment Library Types
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394 ======================
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395
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396 There are numerous library preparation protocols for RNA-seq that result in
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397 sequencing reads with different characteristics. For example, reads can be
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398 single end (only one side of a fragment is recorded as a read) or paired-end
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399 (reads are generated from both ends of a fragment). Further, the sequencing
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400 reads themselves may be unstraned or strand-specific. Finally, paired-end
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401 protocols will have a specified relative orientation. To characterize the
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402 various different typs of sequencing libraries, we've created a miniature
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403 "language" that allows for the succinct description of the many different types
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404 of possible fragment libraries. For paired-end reads, the possible
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405 orientations, along with a graphical description of what they mean, are
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406 illustrated below:
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407 .. image:: ReadLibraryIllustration.png
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408 The library type string consists of three parts: the relative orientation of
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409 the reads, the strandedness of the library, and the directionality of the
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410 reads.
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411 The first part of the library string (relative orientation) is only provided if
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412 the library is paired-end. The possible options are:
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413 ::
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414
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415 I = inward
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416 O = outward
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417 M = matching
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418
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419 The second part of the read library string specifies whether the protocol is
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420 stranded or unstranded; the options are:
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421 ::
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422
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423 S = stranded
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424 U = unstranded
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425
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426 If the protocol is unstranded, then we're done. The final part of the library
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427 string specifies the strand from which the read originates in a strand-specific
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428 protocol — it is only provided if the library is stranded (i.e. if the
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429 library format string is of the form S). The possible values are:
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430 ::
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431
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432 F = read 1 (or single-end read) comes from the forward strand
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433 R = read 1 (or single-end read) comes from the reverse strand
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434
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435 So, for example, if you wanted to specify a fragment library of strand-specific
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436 paired-end reads, oriented toward each other, where read 1 comes from the
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437 forward strand and read 2 comes from the reverse strand, you would specify ``-l
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438 ISF`` on the command line. This designates that the library being processed has
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439 the type "ISF" meaning, **I**\ nward (the relative orientation), **S**\ tranted
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440 (the protocol is strand-specific), **F**\ orward (read 1 comes from the forward
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441 strand).
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442 The single end library strings are a bit simpler than their pair-end counter
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443 parts, since there is no relative orientation of which to speak. Thus, the
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444 only possible library format types for single-end reads are ``U`` (for
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445 unstranded), ``SF`` (for strand-specific reads coming from the forward strand)
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446 and ``SR`` (for strand-specific reads coming from the reverse strand).
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447 A few more examples of some library format strings and their interpretations are:
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448 ::
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449
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450 IU (an unstranded paired-end library where the reads face each other)
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451
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452 ::
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453
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454 SF (a stranded single-end protocol where the reads come from the forward strand)
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455
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456 ::
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457
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458 OSR (a stranded paired-end protocol where the reads face away from each other,
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459 read1 comes from reverse strand and read2 comes from the forward strand)
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460
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461 .. note:: Correspondence to TopHat library types
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462
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463 The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
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464 read aligner has a different convention for specifying the format of the library.
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465 Below is a table that provides the corresponding Salmon/salmon library format
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466 string for each of the potential TopHat library types:
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467
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468 +---------------------+-------------------------+
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469 | TopHat | Salmon (and Sailfish) |
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470 +=====================+============+============+
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471 | | Paired-end | Single-end |
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472 +---------------------+------------+------------+
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473 |``-fr-unstranded`` |``-l IU`` |``-l U`` |
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474 +---------------------+------------+------------+
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475 |``-fr-firststrand`` |``-l ISR`` |``-l SR`` |
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476 +---------------------+------------+------------+
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477 |``-fr-secondstrand`` |``-l ISF`` |``-l SF`` |
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478 +---------------------+------------+------------+
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479
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480 The remaining salmon library format strings are not directly expressible in terms
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481 of the TopHat library types, and so there is no direct mapping for them.
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482 ]]> </help>
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483 <citations>
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484 <citation type="doi">10.1101/021592</citation>
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485 </citations>
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486 </tool>