Mercurial > repos > jjohnson > rsem
annotate rsem_calculate_expression.xml @ 1:1ff2fc8da328
Updates to rsem_calculate_expression.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 05 Dec 2013 10:54:28 -0600 (2013-12-05) |
| parents | 64d45f959303 |
| children | f6b8155ab12a |
| rev | line source |
|---|---|
| 0 | 1 <tool id="rsem_calculate_expression" name="RSEM calculate expression" version="1.1.17"> |
| 2 <description>RNA-Seq by Expectation-Maximization</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.1.17">rsem</requirement> | |
| 5 <requirement type="package" version="0.1.19">samtools</requirement> | |
| 6 <requirement type="package" version="1.0.0">bowtie</requirement> | |
| 7 </requirements> | |
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8 <command> |
| 0 | 9 rsem-calculate-expression |
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10 ## --tag string |
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11 #if $seedlength: |
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12 --seed-length $seedlength |
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13 #end if |
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14 --forward-prob $forward_prob |
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15 #if $rsem_options.fullparams == 'fullset': |
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16 ## Fragment info |
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17 #if $rsem_options.fragment_length_mean: |
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18 --fragment-length-mean $rsem_options.fragment_length_mean |
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19 #end if |
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20 #if $rsem_options.fragment_length_min: |
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21 --fragment-length-min $rsem_options.fragment_length_min |
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22 #end if |
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23 #if $rsem_options.fragment_length_sd: |
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24 --fragment-length-sd $rsem_options.fragment_length_sd |
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25 #end if |
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26 #if $rsem_options.fragment_length_max: |
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27 --fragment-length-max $rsem_options.fragment_length_max |
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28 #end if |
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29 ## RSPD |
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30 #if $rsem_options.rspd.estimate == 'yes': |
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31 --estimate-rspd |
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32 #if $rsem_options.rspd.num_rspd_bins: |
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33 --num-rspd-bins $rsem_options.rspd.num_rspd_bins |
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34 #end if |
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35 #end if |
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36 ## Calculate 95% credibility intervals and posterior mean estimates. |
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37 #if $rsem_options.useci.ci == 'yes': |
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38 --calc-ci |
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39 #if $rsem_options.useci.cimem: |
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40 --ci-memory $rsem_options.useci.cimem |
| 0 | 41 #end if |
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42 #end if |
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43 #end if |
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44 ## --num-threads $GALAXY_SLOTS |
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45 #if $input.format != 'bam' and $input.bowtie_options.fullparams == 'fullset': |
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46 ## Bowtie params |
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47 #if $bowtie_options.bowtie_e: |
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48 --bowtie-e $bowtie_options.bowtie_e |
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49 #end if |
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50 #if $bowtie_options.bowtie_m: |
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51 --bowtie-m $bowtie_options.bowtie_m |
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52 #end if |
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53 #if $bowtie_options.bowtie_n: |
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54 --bowtie-n $bowtie_options.bowtie_n |
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55 #end if |
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56 #end if |
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57 ## Outputs |
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58 #if $rsem_outputs.result_bams == 'none': |
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59 --no-bam-output |
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60 #else |
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61 #if $rsem_outputs.result_bams == 'both': |
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62 --output-genome-bam |
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63 #end if |
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64 $rsem_outputs.sampling_for_bam |
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65 #end if |
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66 ## Input data |
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67 #if $input.format=="fastq" |
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68 $input.fastq_select |
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69 #if $input.fastq.matepair=="single": |
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70 $input.fastq.singlefastq |
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71 #elif $input.fastq.matepair=="paired": |
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72 --paired-end |
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73 $input.fastq.fastq1 |
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74 $input.fastq.fastq2 |
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75 #end if |
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76 #elif $input.format=="fasta" |
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77 --no-qualities |
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78 #if $input.fasta.matepair=="single": |
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79 $input.fasta.singlefasta |
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80 #elif $input.fasta.matepair=="paired": |
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81 --paired-end |
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82 $input.fasta.fasta1 |
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83 $input.fasta.fasta2 |
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84 #end if |
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85 #elif $input.format=="sam" |
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86 #if $input.matepair=="paired": |
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87 --paired-end |
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88 #end if |
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89 #if $input.rsem_sam._extension == 'sam': |
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90 --sam |
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91 #elif $input.rsem_sam._extension == 'bam': |
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92 --bam |
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93 #end if |
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94 $input.rsem_sam |
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95 #end if |
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96 ## RSEM reference |
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97 #if $reference.refSrc == 'history': |
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98 ${reference.rsem_ref.extra_files_path}/${reference.rsem_ref.metadata.reference_name} |
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99 #elif $reference.refSrc == 'cached': |
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100 ${reference.index.fields.path} |
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102 ## sample_name: use a hard coded name so we can pull out galaxy outputs |
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103 rsem_output |
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104 ## direct output into logfile |
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105 > $log |
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106 </command> |
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107 <macros> |
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108 <macro name="rsem_options"> |
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109 <param name="seedlength" type="integer" value="25" optional="true" label="Seed length used by the read aligner" help="Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. RSEM uses this value for Bowtie's seed length parameter. The minimum value is 25. (Default:25)"> |
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110 </param> |
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111 <param name="forward_prob" type="select" label="Is the library strand specific?"> |
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112 <option value="0.5" selected="true">No</option> |
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113 <option value="1">Yes, the reads (or first reads from paired-end libraries) are only in the forward orientation</option> |
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114 <option value="0">Yes, the reads (or first reads from paired-end libraries) are only in the reverse orientation</option> |
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115 </param> |
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116 <conditional name="rsem_options"> |
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117 <param name="fullparams" type="select" label="Additional RSEM options"> |
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118 <option value="default">Use RSEM Defaults</option> |
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119 <option value="fullset">Set Additional RSEM Options</option> |
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120 </param> |
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121 <when value="default"/> |
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122 <when value="fullset"> |
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123 <param name="fragment_length_min" type="integer" value="1" optional="true" label="Minimum read/insert length." help=" This is also the value for the bowtie -I option"> |
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124 <validator type="in_range" message="0 or greater" min="0" /> |
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125 </param> |
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126 <param name="fragment_length_max" type="integer" value="1000" optional="true" label="Maximum read/insert length." help=" This is also the value for the bowtie -X option"> |
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127 <validator type="in_range" message="0 or greater" min="0" max="1000000"/> |
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128 </param> |
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129 <param name="fragment_length_mean" type="float" value="" optional="true" label="Fragment length mean (single-end data only)" help="The mean of the fragment length distribution, which is assumed to be a Gaussian. (Default: -1, which disables use of the fragment length distribution)"> |
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130 </param> |
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131 <param name="fragment_length_sd" type="float" value="" optional="true" label="The standard deviation of the fragment length distribution (single-end data only)" help="Default 0, which assumes that all fragments are of the same length, given by the rounded value of fragment length mean. "> |
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132 </param> |
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133 <conditional name="rspd"> |
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134 <param name="estimate" type="select" lanel="Read Start Position Distribution (RSPD)" |
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135 help="Set this option if you want to estimate the read start position distribution (RSPD) from data. Otherwise, RSEM will use a uniform RSPD."> |
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136 <option value="no" selected="true">Use a uniform RSPD</option> |
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137 <option value="yes">Estimate and correct for a non-uniform RSPD</option> |
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138 </param> |
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139 <when value="no"/> |
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140 <when value="yes"> |
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141 <param name="num_rspd_bins" type="integer" value="20" optional="true" label="Number of bins in the RSPD." help="Use of the default setting of 20 is recommended."> |
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142 <validator type="in_range" message="" min="0" max="100"/> |
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143 </param> |
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144 </when> |
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145 </conditional> |
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146 <conditional name="useci"> |
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147 <param name="ci" type="select" label="Calculate 95% Credibility Intervals"> |
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148 <option value="no" selected="true">no</option> |
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149 <option value="yes">yes</option> |
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150 </param> |
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151 <when value="no"/> |
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152 <when value="yes"> |
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153 <param name="cimem" size="4" type="text" value="1024" label="Amount of memory in (MB) for computing CI" /> |
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154 </when> |
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155 </conditional> |
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156 </when> |
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157 </conditional> |
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158 </macro> |
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159 <macro name="bowtie_options"> |
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160 <conditional name="bowtie_options"> |
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161 <param name="fullparams" type="select" label="bowtie settings"> |
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162 <option value="default">use bowtie defaults</option> |
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163 <option value="fullset">set bowtie options</option> |
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164 </param> |
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165 <when value="default"/> |
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166 <when value="fullset"> |
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167 <param name="bowtie_n" type="integer" value="2" optional="true" label="Bowtie mismatches" help="Bowtie parameter max # of mismatches in the seed. (Range: 0-3, Default: 2) "> |
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168 <validator type="in_range" message="max # of mismatches in the seed between 0 and 3" min="0" max="3"/> |
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169 </param> |
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170 <param name="bowtie_e" type="integer" value="99999999" label="Maximum sum of quality scores at mismatched positions in read alignments. This is also the value for the Bowtie -e option"> |
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171 </param> |
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172 <param name="bowtie_m" type="integer" value="200" label="Discard alignments for reads with number of alignments greater than"> |
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173 </param> |
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174 </when> |
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175 </conditional> |
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176 </macro> |
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177 <macro name="sampling_for_bam"> |
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178 <param name="sampling_for_bam" type="boolean" truevalue="--sampling-for-bam" falsevalue="" checked="false" label="Use sampling for BAM"> |
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179 <help> When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off) |
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180 </help> |
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181 </param> |
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182 </macro> |
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183 </macros> |
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185 <inputs> |
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186 <param name="sample" type="text" value="rsem_sample" label="Sample name" /> |
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187 <conditional name="reference"> |
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188 <param name="refSrc" type="select" label="RSEM Reference"> |
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189 <option value="cached">Locally cached</option> |
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190 <option value="history">From your history</option> |
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191 </param> |
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192 <when value="cached"> |
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193 <param name="index" type="select" label="Select RSEM reference" help="Select from a list of pre-indexed references. If you don't see anything consult the wrapper's documentation on how to create or download a reference"> |
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194 <options from_data_table="rsem_indexes"> |
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195 <filter type="sort_by" column="2" /> |
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196 <validator type="no_options" message="No indexes are available" /> |
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197 </options> |
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198 </param> |
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199 </when> |
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200 <when value="history"> |
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201 <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" /> |
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202 </when> |
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204 <conditional name="input"> |
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205 <param name="format" type="select" label="RSEM Input file type"> |
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206 <option value="fastq">FASTQ</option> |
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207 <option value="fasta">FASTA</option> |
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208 <option value="sam">SAM/BAM</option> |
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209 </param> |
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210 <when value="fastq"> |
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211 <param name="fastq_select" size="15" type="select" label="FASTQ type" > |
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212 <option value="--phred33-quals">phred33 qualities (default for sanger)</option> |
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213 <option value="--solexa-quals">solexa qualities</option> |
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214 <option value="--phred64-quals">phred64 qualities</option> |
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215 </param> |
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216 <conditional name="fastq"> |
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217 <param name="matepair" type="select" label="Library type"> |
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218 <option value="single">Single End Reads</option> |
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219 <option value="paired">Paired End Reads</option> |
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220 </param> |
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221 <when value="single"> |
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222 <param name="singlefastq" type="data" format="fastq" label="FASTQ file" /> |
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223 </when> |
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224 <when value="paired"> |
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225 <param name="fastq1" type="data" format="fastq" label="Read 1 fastq file" /> |
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226 <param name="fastq2" type="data" format="fastq" label="Read 2 fastq file" /> |
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227 </when> |
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228 </conditional> |
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229 <expand macro="bowtie_options"/> |
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230 </when> |
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231 <when value="fasta"> |
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232 <conditional name="fasta"> |
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233 <param name="matepair" type="select" label="Library Type"> |
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234 <option value="single">Single End Reads</option> |
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235 <option value="paired">Paired End Reads</option> |
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236 </param> |
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237 <when value="single"> |
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238 <param name="singlefasta" type="data" format="fasta" label="fasta file" /> |
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239 </when> |
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240 <when value="paired"> |
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241 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" /> |
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242 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" /> |
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243 </when> |
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244 </conditional> |
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245 <expand macro="bowtie_options"/> |
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246 </when> |
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247 <when value="sam"> |
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248 <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam --> |
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249 <param name="matepair" type="select" label="Library Type"> |
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250 <option value="single">Single End Reads</option> |
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251 <option value="paired">Paired End Reads</option> |
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252 </param> |
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253 <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" /> |
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254 </when> |
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255 </conditional> |
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256 <expand macro="rsem_options"/> |
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257 <conditional name="rsem_outputs"> |
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258 <param name="result_bams" type="select" label="Create bam results files" |
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259 help="In addition to the transcript-coordinate-based BAM file output, also output a BAM file with the read alignments in genomic coordinates" > |
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260 <option value="none">No BAM results files</option> |
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261 <option value="default" selected="true">Transcript BAM results file</option> |
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262 <option value="both">Transcript and genome BAM results files</option> |
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263 </param> |
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264 <when value="none"/> |
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265 <when value="default"> |
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266 <expand macro="sampling_for_bam"/> |
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267 </when> |
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268 <when value="both"> |
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269 <expand macro="sampling_for_bam"/> |
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270 </when> |
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271 </conditional> |
| 0 | 272 </inputs> |
| 273 <stdio> | |
| 274 <exit_code range="1:" level="fatal" description="Error Running RSEM" /> | |
| 275 </stdio> | |
| 276 <outputs> | |
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277 <data format="tabular" name="output" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/> |
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278 <data format="tabular" name="isoforms" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/> |
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279 <data format="bam" name="transcript_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.bam" > |
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280 <filter>rsem_outputs['result_bams'] != "none"</filter> |
| 0 | 281 </data> |
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282 <data format="bam" name="transcript__sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" > |
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283 <filter>rsem_outputs['result_bams'] != "none"</filter> |
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284 </data> |
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285 <data format="bam" name="genome_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.bam"> |
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286 <filter>rsem_outputs['result_bams'] == "both"</filter> |
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287 </data> |
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288 <data format="bam" name="genome_sorted_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.sorted.bam"> |
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289 <filter>rsem_outputs['result_bams'] == "both"</filter> |
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290 </data> |
| 0 | 291 <data format="txt" name="log" label="${sample}.rsem_log"/> |
| 292 </outputs> | |
| 293 <help> | |
| 294 | |
| 295 | |
| 296 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/ | |
| 297 | |
| 298 NAME | |
| 299 rsem-calculate-expression | |
| 300 | |
| 301 SYNOPSIS | |
| 302 rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name | |
| 303 rsem-calculate-expression [options] --paired-end upstream_read_file/s downstream_read_file/s reference_name sample_name | |
| 304 rsem-calculate-expression [options] --sam/--bam [--paired-end] input reference_name sample_name | |
| 305 | |
| 306 ARGUMENTS | |
| 307 upstream_read_files/s | |
| 308 Comma-separated list of files containing single-end reads or | |
| 309 upstream reads for paired-end data. By default, these files are | |
| 310 assumed to be in FASTQ format. If the --no-qualities option is | |
| 311 specified, then FASTA format is expected. | |
| 312 | |
| 313 downstream_read_file/s | |
| 314 Comma-separated list of files containing downstream reads which are | |
| 315 paired with the upstream reads. By default, these files are assumed | |
| 316 to be in FASTQ format. If the --no-qualities option is specified, | |
| 317 then FASTA format is expected. | |
| 318 | |
| 319 input | |
| 320 SAM/BAM formatted input file. If "-" is specified for the filename, | |
| 321 SAM/BAM input is instead assumed to come from standard input. RSEM | |
| 322 requires all alignments of the same read group together. For | |
| 323 paired-end reads, RSEM also requires the two mates of any alignment | |
| 324 be adjacent. See Description section for how to make input file obey | |
| 325 RSEM's requirements. | |
| 326 | |
| 327 reference_name | |
| 328 The name of the reference used. The user must have run | |
| 329 'rsem-prepare-reference' with this reference_name before running | |
| 330 this program. | |
| 331 | |
| 332 sample_name | |
| 333 The name of the sample analyzed. All output files are prefixed by | |
| 334 this name (e.g., sample_name.genes.results) | |
| 335 | |
| 336 OPTIONS | |
| 337 | |
| 338 --paired-end | |
| 339 Input reads are paired-end reads. (Default: off) | |
| 340 | |
| 341 --no-qualities | |
| 342 Input reads do not contain quality scores. (Default: off) | |
| 343 | |
| 344 --strand-specific | |
| 345 The RNA-Seq protocol used to generate the reads is strand specific, | |
| 346 i.e., all (upstream) reads are derived from the forward strand. This | |
| 347 option is equivalent to --forward-prob=1.0. With this option set, if | |
| 348 RSEM runs the Bowtie aligner, the '--norc' Bowtie option will be | |
| 349 used, which disables alignment to the reverse strand of transcripts. | |
| 350 (Default: off) | |
| 351 | |
| 352 --sam | |
| 353 Input file is in SAM format. (Default: off) | |
| 354 | |
| 355 --bam | |
| 356 Input file is in BAM format. (Default: off) | |
| 357 | |
| 358 --sam-header-info [file] | |
| 359 RSEM reads header information from input by default. If this option | |
| 360 is on, header information is read from the specified file. For the | |
| 361 format of the file, please see SAM official website. (Default: "") | |
| 362 | |
| 363 -p/--num-threads [int] | |
| 364 Number of threads to use. Both Bowtie and expression estimation will | |
| 365 use this many threads. (Default: 1) | |
| 366 | |
| 367 --no-bam-output | |
| 368 Do not output any BAM file. (Default: off) | |
| 369 | |
| 370 --output-genome-bam | |
| 371 Generate a BAM file, 'sample_name.genome.bam', with alignments | |
| 372 mapped to genomic coordinates and annotated with their posterior | |
| 373 probabilities. In addition, RSEM will call samtools (included in | |
| 374 RSEM package) to sort and index the bam file. | |
| 375 'sample_name.genome.sorted.bam' and | |
| 376 'sample_name.genome.sorted.bam.bai' will be generated. (Default: | |
| 377 off) | |
| 378 | |
| 379 --sampling-for-bam | |
| 380 When RSEM generates a BAM file, instead of outputing all alignments | |
| 381 a read has with their posterior probabilities, one alignment is | |
| 382 sampled and outputed according to the posterior probabilities. If | |
| 383 the sampling result is that the read comes from the "noise" | |
| 384 transcript, nothing is outputed. (Default: off) | |
| 385 | |
| 386 --calc-ci | |
| 387 Calculate 95% credibility intervals and posterior mean estimates. | |
| 388 (Default: off) | |
| 389 | |
| 390 --seed-length [int] | |
| 391 Seed length used by the read aligner. Providing the correct value is | |
| 392 important for RSEM. If RSEM runs Bowtie, it uses this value for | |
| 393 Bowtie's seed length parameter. Any read with its or at least one of | |
| 394 its mates' (for paired-end reads) length less than this value will | |
| 395 be ignored. If the references are not added poly(A) tails, the | |
| 396 minimum allowed value is 5, otherwise, the minimum allowed value is | |
| 397 25. Note that this script will only check if the value less or equal than | |
| 398 5 and give a warning message if the value less than 25 but greter or equal than | |
| 399 5. (Default: 25) | |
| 400 | |
| 401 --tag [string] | |
| 402 The name of the optional field used in the SAM input for identifying | |
| 403 a read with too many valid alignments. The field should have the | |
| 404 format [tagName]:i:[value], where a [value] bigger than 0 indicates | |
| 405 a read with too many alignments. (Default: "") | |
| 406 | |
| 407 --bowtie-path [path] | |
| 408 The path to the bowtie executables. (Default: the path to the bowtie | |
| 409 executables is assumed to be in the user's PATH environment | |
| 410 variable) | |
| 411 | |
| 412 --bowtie-n [int] | |
| 413 (Bowtie parameter) max # of mismatches in the seed. (Range: 0-3, | |
| 414 Default: 2) | |
| 415 | |
| 416 --bowtie-e [int] | |
| 417 (Bowtie parameter) max sum of mismatch quality scores across the | |
| 418 alignment. (Default: 99999999) | |
| 419 | |
| 420 --bowtie-m [int] | |
| 421 (Bowtie parameter) suppress all alignments for a read if greater then [int] | |
| 422 valid alignments exist. (Default: 200) | |
| 423 | |
| 424 --bowtie-chunkmbs [int] | |
| 425 (Bowtie parameter) memory allocated for best first alignment | |
| 426 calculation (Default: 0 - use bowtie's default) | |
| 427 | |
| 428 --phred33-quals | |
| 429 Input quality scores are encoded as Phred+33. (Default: on) | |
| 430 | |
| 431 --phred64-quals | |
| 432 Input quality scores are encoded as Phred+64 (default for GA | |
| 433 Pipeline ver. less than 1.3). (Default: off) | |
| 434 | |
| 435 --solexa-quals | |
| 436 Input quality scores are solexa encoded (from GA Pipeline ver. less | |
| 437 than 1.3). (Default: off) | |
| 438 | |
| 439 --forward-prob [double] | |
| 440 Probability of generating a read from the forward strand of a | |
| 441 transcript. Set to 1 for a strand-specific protocol where all | |
| 442 (upstream) reads are derived from the forward strand, 0 for a | |
| 443 strand-specific protocol where all (upstream) read are derived from | |
| 444 the reverse strand, or 0.5 for a non-strand-specific protocol. | |
| 445 (Default: 0.5) | |
| 446 | |
| 447 --fragment-length-min [int] | |
| 448 Minimum read/insert length allowed. This is also the value for the | |
| 449 bowtie -I option. (Default: 1) | |
| 450 | |
| 451 --fragment-length-max [int] | |
| 452 Maximum read/insert length allowed. This is also the value for the | |
| 453 bowtie -X option. (Default: 1000) | |
| 454 | |
| 455 --fragment-length-mean [double] | |
| 456 (single-end data only) The mean of the fragment length distribution, | |
| 457 which is assumed to be a Gaussian. (Default: -1, which disables use | |
| 458 of the fragment length distribution) | |
| 459 | |
| 460 --fragment-length-sd [double] | |
| 461 (single-end data only) The standard deviation of the fragment length | |
| 462 distribution, which is assumed to be a Gaussian. (Default: 0, which | |
| 463 assumes that all fragments are of the same length, given by the | |
| 464 rounded value of --fragment-length-mean) | |
| 465 | |
| 466 --estimate-rspd | |
| 467 Set this option if you want to estimate the read start position | |
| 468 distribution (RSPD) from data. Otherwise, RSEM will use a uniform | |
| 469 RSPD. (Default: off) | |
| 470 | |
| 471 --num-rspd-bins [int] | |
| 472 Number of bins in the RSPD. Only relevant when '--estimate-rspd' is | |
| 473 specified. Use of the default setting is recommended. (Default: 20) | |
| 474 | |
| 475 --ci-memory [int] | |
| 476 Maximum size (in memory, MB) of the auxiliary buffer used for | |
| 477 computing credibility intervals (CI). Set it larger for a faster CI | |
| 478 calculation. However, leaving 2 GB memory free for other usage is | |
| 479 recommended. (Default: 1024) | |
| 480 | |
| 481 --keep-intermediate-files | |
| 482 Keep temporary files generated by RSEM. RSEM creates a temporary | |
| 483 directory, 'sample_name.temp', into which it puts all intermediate | |
| 484 output files. If this directory already exists, RSEM overwrites all | |
| 485 files generated by previous RSEM runs inside of it. By default, | |
| 486 after RSEM finishes, the temporary directory is deleted. Set this | |
| 487 option to prevent the deletion of this directory and the | |
| 488 intermediate files inside of it. (Default: off) | |
| 489 | |
| 490 --time | |
| 491 Output time consumed by each step of RSEM to 'sample_name.time'. | |
| 492 (Default: off) | |
| 493 | |
| 494 -q/--quiet | |
| 495 Suppress the output of logging information. (Default: off) | |
| 496 | |
| 497 -h/--help | |
| 498 Show help information. | |
| 499 | |
| 500 DESCRIPTION | |
| 501 In its default mode, this program aligns input reads against a reference | |
| 502 transcriptome with Bowtie and calculates expression values using the | |
| 503 alignments. RSEM assumes the data are single-end reads with quality | |
| 504 scores, unless the '--paired-end' or '--no-qualities' options are | |
| 505 specified. Users may use an alternative aligner by specifying one of the | |
| 506 --sam and --bam options, and providing an alignment file in the | |
| 507 specified format. However, users should make sure that they align | |
| 508 against the indices generated by 'rsem-prepare-reference' and the | |
| 509 alignment file satisfies the requirements mentioned in ARGUMENTS | |
| 510 section. | |
| 511 | |
| 512 One simple way to make the alignment file satisfying RSEM's requirements | |
| 513 (assuming the aligner used put mates in a paired-end read adjacent) is | |
| 514 to use 'convert-sam-for-rsem' script. This script only accept SAM format | |
| 515 files as input. If a BAM format file is obtained, please use samtools to | |
| 516 convert it to a SAM file first. For example, if '/ref/mouse_125' is the | |
| 517 'reference_name' and the SAM file is named 'input.sam', you can run the | |
| 518 following command: | |
| 519 | |
| 520 convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam | |
| 521 | |
| 522 For details, please refer to 'convert-sam-for-rsem's documentation page. | |
| 523 | |
| 524 The SAM/BAM format RSEM uses is v1.4. However, it is compatible with old | |
| 525 SAM/BAM format. However, RSEM cannot recognize 0x100 in the FLAG field. | |
| 526 In addition, RSEM requires SEQ and QUAL are not '*'. | |
| 527 | |
| 528 The user must run 'rsem-prepare-reference' with the appropriate | |
| 529 reference before using this program. | |
| 530 | |
| 531 For single-end data, it is strongly recommended that the user provide | |
| 532 the fragment length distribution parameters (--fragment-length-mean and | |
| 533 --fragment-length-sd). For paired-end data, RSEM will automatically | |
| 534 learn a fragment length distribution from the data. | |
| 535 | |
| 536 Please note that some of the default values for the Bowtie parameters | |
| 537 are not the same as those defined for Bowtie itself. | |
| 538 | |
| 539 The temporary directory and all intermediate files will be removed when | |
| 540 RSEM finishes unless '--keep-intermediate-files' is specified. | |
| 541 | |
| 542 With the '--calc-ci' option, 95% credibility intervals and posterior | |
| 543 mean estimates will be calculated in addition to maximum likelihood | |
| 544 estimates. | |
| 545 | |
| 546 OUTPUT | |
| 547 sample_name.genes.results | |
| 548 File containing gene level expression estimates. The format of each | |
| 549 line in this file is: | |
| 550 | |
| 551 gene_id expected_counts tau_value [pmc_value tau_pme_value | |
| 552 tau_ci_lower_bound tau_ci_upper_bound] transcript_id_list | |
| 553 | |
| 554 Fields are separated by the tab character. Fields within "[]" are | |
| 555 only presented if '--calc-ci' is set. pme stands for posterior mean | |
| 556 estimation. pmc stands for posterior mean counts. ci_lower_bound(l) | |
| 557 means the lower bound of the credibility intervals, | |
| 558 ci_upper_bound(u) means the upper bound of the credibility | |
| 559 intervals. So the credibility interval is [l, u]. | |
| 560 'transcript_id_list' is a space-separated list of transcript_ids | |
| 561 belonging to the gene. If no gene information is provided, this file | |
| 562 has the same content as 'sample_name.isoforms.results'. | |
| 563 | |
| 564 sample_name.isoforms.results | |
| 565 File containing isoform level expression values. The format of each | |
| 566 line in this file is: | |
| 567 | |
| 568 transcript_id expected_counts tau_value [pmc_value tau_pme_value | |
| 569 tau_ci_lower_bound tau_ci_upper_bound] gene_id | |
| 570 | |
| 571 Fields are separated by the tab character. 'gene_id' is the gene_id | |
| 572 of the gene which this transcript belongs to. If no gene information | |
| 573 is provided, 'gene_id' and 'transcript_id' are the same. | |
| 574 | |
| 575 sample_name.transcript.bam, sample_name.transcript.sorted.bam and | |
| 576 sample_name.transcript.sorted.bam.bai | |
| 577 Only generated when --no-bam-output is not specified. | |
| 578 | |
| 579 'sample_name.transcript.bam' is a BAM-formatted file of read | |
| 580 alignments in transcript coordinates. The MAPQ field of each | |
| 581 alignment is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)), | |
| 582 where w is the posterior probability of that alignment being the | |
| 583 true mapping of a read. In addition, RSEM pads a new tag ZW:f:value, | |
| 584 where value is a single precision floating number representing the | |
| 585 posterior probability. | |
| 586 | |
| 587 'sample_name.transcript.sorted.bam' and | |
| 588 'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and | |
| 589 indices generated by samtools (included in RSEM package). | |
| 590 | |
| 591 sample_name.genome.bam, sample_name.genome.sorted.bam and | |
| 592 sample_name.genome.sorted.bam.bai | |
| 593 Only generated when --no-bam-output is not specified and | |
| 594 --output-genome-bam is specified. | |
| 595 | |
| 596 'sample_name.genome.bam' is a BAM-formatted file of read alignments | |
| 597 in genomic coordinates. Alignments of reads that have identical | |
| 598 genomic coordinates (i.e., alignments to different isoforms that | |
| 599 share the same genomic region) are collapsed into one alignment. The | |
| 600 MAPQ field of each alignment is set to min(100, floor(-10 * | |
| 601 log10(1.0 - w) + 0.5)), where w is the posterior probability of that | |
| 602 alignment being the true mapping of a read. In addition, RSEM pads a | |
| 603 new tag ZW:f:value, where value is a single precision floating | |
| 604 number representing the posterior probability. If an alignment is | |
| 605 spliced, a XS:A:value tag is also added, where value is either '+' | |
| 606 or '-' indicating the strand of the transcript it aligns to. | |
| 607 | |
| 608 'sample_name.genome.sorted.bam' and | |
| 609 'sample_name.genome.sorted.bam.bai' are the sorted BAM file and | |
| 610 indices generated by samtools (included in RSEM package). | |
| 611 | |
| 612 sample_name.sam.gz | |
| 613 Only generated when the input files are raw reads instead of SAM/BAM | |
| 614 format files | |
| 615 | |
| 616 It is the gzipped SAM output produced by bowtie aligner. | |
| 617 | |
| 618 sample_name.time | |
| 619 Only generated when --time is specified. | |
| 620 | |
| 621 It contains time (in seconds) consumed by aligning reads, estimating | |
| 622 expression levels and calculating credibility intervals. | |
| 623 | |
| 624 sample_name.stat | |
| 625 This is a folder instead of a file. All model related statistics are | |
| 626 stored in this folder. Use 'rsem-plot-model' can generate plots | |
| 627 using this folder. | |
| 628 | |
| 629 EXAMPLES | |
| 630 Assume the path to the bowtie executables is in the user's PATH | |
| 631 environment variable. Reference files are under '/ref' with name | |
| 632 'mouse_125'. | |
| 633 | |
| 634 1) '/data/mmliver.fq', single-end reads with quality scores. Quality | |
| 635 scores are encoded as for 'GA pipeline version >= 1.3'. We want to use 8 | |
| 636 threads and generate a genome BAM file: | |
| 637 | |
| 638 rsem-calculate-expression --phred64-quals \ | |
| 639 -p 8 \ | |
| 640 --output-genome-bam \ | |
| 641 /data/mmliver.fq \ | |
| 642 /ref/mouse_125 \ | |
| 643 mmliver_single_quals | |
| 644 | |
| 645 2) '/data/mmliver_1.fq' and '/data/mmliver_2.fq', paired-end reads with | |
| 646 quality scores. Quality scores are in SANGER format. We want to use 8 | |
| 647 threads and do not generate a genome BAM file: | |
| 648 | |
| 649 rsem-calculate-expression -p 8 \ | |
| 650 --paired-end \ | |
| 651 /data/mmliver_1.fq \ | |
| 652 /data/mmliver_2.fq \ | |
| 653 /ref/mouse_125 \ | |
| 654 mmliver_paired_end_quals | |
| 655 | |
| 656 3) '/data/mmliver.fa', single-end reads without quality scores. We want | |
| 657 to use 8 threads: | |
| 658 | |
| 659 rsem-calculate-expression -p 8 \ | |
| 660 --no-qualities \ | |
| 661 /data/mmliver.fa \ | |
| 662 /ref/mouse_125 \ | |
| 663 mmliver_single_without_quals | |
| 664 | |
| 665 4) Data are the same as 1). We want to take a fragment length | |
| 666 distribution into consideration. We set the fragment length mean to 150 | |
| 667 and the standard deviation to 35. In addition to a BAM file, we also | |
| 668 want to generate credibility intervals. We allow RSEM to use 1GB of | |
| 669 memory for CI calculation: | |
| 670 | |
| 671 rsem-calculate-expression --bowtie-path /sw/bowtie \ | |
| 672 --phred64-quals \ | |
| 673 --fragment-length-mean 150.0 \ | |
| 674 --fragment-length-sd 35.0 \ | |
| 675 -p 8 \ | |
| 676 --output-genome-bam \ | |
| 677 --calc-ci \ | |
| 678 --ci-memory 1024 \ | |
| 679 /data/mmliver.fq \ | |
| 680 /ref/mouse_125 \ | |
| 681 mmliver_single_quals | |
| 682 | |
| 683 5) '/data/mmliver_paired_end_quals.bam', paired-end reads with quality | |
| 684 scores. We want to use 8 threads: | |
| 685 | |
| 686 rsem-calculate-expression --paired-end \ | |
| 687 --bam \ | |
| 688 -p 8 \ | |
| 689 /data/mmliver_paired_end_quals.bam \ | |
| 690 /ref/mouse_125 \ | |
| 691 mmliver_paired_end_quals | |
| 692 </help> | |
| 693 </tool> |