Mercurial > repos > devteam > cuffcompare
annotate cuffcompare_wrapper.xml @ 9:e66b9b5b8580 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
| author | devteam |
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| date | Sun, 19 Feb 2017 12:12:05 -0500 |
| parents | 1322b73ffe44 |
| children | f648e5180e40 |
| rev | line source |
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e66b9b5b8580
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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1 <tool id="cuffcompare" name="Cuffcompare" version="@VERSION@.1"> |
| 0 | 2 <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description> |
| 6 | 3 <macros> |
| 4 <import>cuff_macros.xml</import> | |
| 5 </macros> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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6 <expand macro="requirements" /> |
| 0 | 7 <version_command>cuffcompare 2>&1 | head -n 1</version_command> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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8 <command detect_errors="aggressive"><![CDATA[ |
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1322b73ffe44
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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9 python '$__tool_directory__/cuffcompare_wrapper.py' |
| 0 | 10 ## Use annotation reference? |
| 11 #if $annotation.use_ref_annotation == "Yes": | |
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1322b73ffe44
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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12 -r '$annotation.reference_annotation' |
| 0 | 13 #if $annotation.ignore_nonoverlapping_reference: |
| 14 -R | |
| 15 #end if | |
| 6 | 16 #if $annotation.ignore_nonoverlapping_transfrags: |
| 17 -Q | |
| 18 #end if | |
| 19 | |
| 0 | 20 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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21 |
| 0 | 22 ## Use sequence data? |
| 23 #if $seq_data.use_seq_data == "Yes": | |
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24 -s |
| 0 | 25 #if $seq_data.seq_source.index_source == "history": |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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26 --ref_file '$seq_data.seq_source.ref_file' |
| 0 | 27 #else: |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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28 --index '${seq_data.seq_source.index.fields.path}' |
| 0 | 29 #end if |
| 30 #end if | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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31 |
| 6 | 32 $discard_single_exon |
| 33 | |
| 34 -e $max_dist_exon | |
| 35 -d $max_dist_group | |
| 36 | |
| 37 #if $discard_intron_redundant_transfrags: | |
| 38 -F | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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39 #end if |
| 6 | 40 |
| 0 | 41 ## Outputs. |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
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42 --combined-transcripts '${transcripts_combined}' |
| 6 | 43 |
| 44 @CUFFLINKS_GTF_INPUTS@ | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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45 ]]></command> |
| 0 | 46 <inputs> |
| 6 | 47 <expand macro="cufflinks_gtf_inputs" /> |
| 0 | 48 <conditional name="annotation"> |
| 49 <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> | |
| 50 <option value="No">No</option> | |
| 51 <option value="Yes">Yes</option> | |
| 52 </param> | |
| 53 <when value="Yes"> | |
| 6 | 54 <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/> |
| 55 <param name="ignore_nonoverlapping_reference" type="boolean" label="Ignore reference transcripts that are not overlapped by any input transfrags" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" /> | |
| 56 <param name="ignore_nonoverlapping_transfrags" type="boolean" label="Ignore input transcripts that are not overlapped by any reference transcripts" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all 'novel' loci!" /> | |
| 0 | 57 </when> |
| 58 <when value="No"> | |
| 59 </when> | |
| 60 </conditional> | |
| 61 <conditional name="seq_data"> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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62 <param name="use_seq_data" type="select" label="Use Sequence Data" |
| 6 | 63 help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff."> |
| 0 | 64 <option value="Yes">Yes</option> |
| 65 <option value="No">No</option> | |
| 66 </param> | |
| 67 <when value="No"></when> | |
| 68 <when value="Yes"> | |
| 69 <conditional name="seq_source"> | |
| 70 <param name="index_source" type="select" label="Choose the source for the reference list"> | |
| 71 <option value="cached">Locally cached</option> | |
| 72 <option value="history">History</option> | |
| 73 </param> | |
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74 <when value="cached"> |
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75 <param name="index" type="select" label="Using reference genome"> |
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76 <options from_data_table="fasta_indexes"> |
| 6 | 77 <filter type="data_meta" ref="inputs" key="dbkey" column="1" /> |
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78 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> |
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79 </options> |
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80 </param> |
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81 </when> |
| 0 | 82 <when value="history"> |
| 83 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
| 84 </when> | |
| 85 </conditional> | |
| 86 </when> | |
| 87 </conditional> | |
| 6 | 88 <param type="select" name="discard_single_exon" label="discard (ignore) single-exon transcripts"> |
| 89 <option value="" selected="True">No</option> | |
| 90 <option value="-M">Discard single-exon transfrags and reference transcripts</option> | |
| 91 <option value="-N">Discard single-exon reference transcripts</option> | |
| 92 </param> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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93 <param type="integer" name="max_dist_exon" value="100" label="Max. Distance for assessing exon accuracy" |
| 6 | 94 help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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95 <param type="integer" name="max_dist_group" value="100" label="Max.Distance for transcript grouping" |
| 6 | 96 help="max. distance (range) for grouping transcript start sites. Default: 100" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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97 <param type="boolean" name="discard_intron_redundant_transfrags" label="discard intron-redundant transfrags sharing 5'" |
| 6 | 98 help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" /> |
| 0 | 99 </inputs> |
| 100 | |
| 101 <outputs> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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102 <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" |
| 0 | 103 from_work_dir="cc_output.stats" /> |
| 6 | 104 <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tmap file" |
| 0 | 105 from_work_dir="cc_output.input1.tmap" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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106 <data format="tabular" name="input1_refmap" |
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e66b9b5b8580
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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107 label="${tool.name} on ${on_string}: data ${inputs[0].hid} refmap file" |
| 0 | 108 from_work_dir="cc_output.input1.refmap"> |
| 109 <filter>annotation['use_ref_annotation'] == 'Yes'</filter> | |
| 110 </data> | |
| 6 | 111 <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${inputs[1].hid} tmap file" from_work_dir="cc_output.input2.tmap"> |
| 112 <filter>@HAS_MULTIPLE_INPUTS@</filter> | |
| 0 | 113 </data> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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114 <data format="tabular" name="input2_refmap" |
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e66b9b5b8580
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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115 label="${tool.name} on ${on_string}: data ${inputs[1].hid} refmap file" |
| 0 | 116 from_work_dir="cc_output.input2.refmap"> |
| 6 | 117 <filter>annotation['use_ref_annotation'] == 'Yes' and @HAS_MULTIPLE_INPUTS@</filter> |
| 0 | 118 </data> |
| 119 <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking"> | |
| 6 | 120 <filter>@HAS_MULTIPLE_INPUTS@</filter> |
| 0 | 121 </data> |
| 122 <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/> | |
| 123 </outputs> | |
| 124 | |
| 125 <tests> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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126 <!-- |
| 0 | 127 cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf |
| 128 --> | |
| 129 <test> | |
| 6 | 130 <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/> |
| 0 | 131 <param name="use_ref_annotation" value="Yes"/> |
| 132 <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> | |
| 133 <param name="ignore_nonoverlapping_reference" value="Yes"/> | |
| 6 | 134 <param name="ignore_nonoverlapping_transfrags" value="No"/> |
| 0 | 135 <param name="use_seq_data" value="No"/> |
| 6 | 136 <param name="discard_single_exon" value="" /> |
| 137 <param name="max_dist_exon" value="100" /> | |
| 138 <param name="max_dist_group" value="100" /> | |
| 139 <param name="discard_intron_redundant_transfrags" value="No" /> | |
| 0 | 140 <!-- Line diffs are the result of different locations for input files; this cannot be fixed as cuffcompare outputs |
| 141 full input path for each input. --> | |
| 6 | 142 <output name="transcripts_accuracy" file="cuffcompare_out7.txt" lines_diff="2"/> |
| 0 | 143 <output name="input1_tmap" file="cuffcompare_out1.tmap"/> |
| 144 <output name="input1_refmap" file="cuffcompare_out2.refmap"/> | |
| 145 <output name="input2_tmap" file="cuffcompare_out3.tmap"/> | |
| 146 <output name="input2_refmap" file="cuffcompare_out4.refmap"/> | |
| 147 <output name="transcripts_tracking" file="cuffcompare_out6.tracking"/> | |
| 148 <output name="transcripts_combined" file="cuffcompare_out5.gtf"/> | |
| 149 </test> | |
| 150 </tests> | |
| 151 | |
| 152 <help> | |
| 153 **Cuffcompare Overview** | |
| 154 | |
| 155 Cuffcompare is part of Cufflinks_. Cuffcompare helps you: (a) compare your assembled transcripts to a reference annotation and (b) track Cufflinks transcripts across multiple experiments (e.g. across a time course). Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 | |
| 156 | |
| 6 | 157 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/ |
| 158 | |
| 0 | 159 ------ |
| 160 | |
| 161 **Know what you are doing** | |
| 162 | |
| 163 .. class:: warningmark | |
| 164 | |
| 165 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. | |
| 166 | |
| 6 | 167 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/ |
| 0 | 168 |
| 169 ------ | |
| 170 | |
| 171 **Input format** | |
| 172 | |
| 173 Cuffcompare takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) | |
| 174 | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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175 .. _Ensembl: http://www.ensembl.org |
| 0 | 176 |
| 177 ------ | |
| 178 | |
| 179 **Outputs** | |
| 180 | |
| 181 Cuffcompare produces the following output files: | |
| 182 | |
| 183 Transcripts Accuracy File: | |
| 184 | |
| 185 Cuffcompare reports various statistics related to the "accuracy" of the transcripts in each sample when compared to the reference annotation data. The typical gene finding measures of "sensitivity" and "specificity" (as defined in Burset, M., Guigó, R. : Evaluation of gene structure prediction programs (1996) Genomics, 34 (3), pp. 353-367. doi: 10.1006/geno.1996.0298) are calculated at various levels (nucleotide, exon, intron, transcript, gene) for each input file and reported in this file. The Sn and Sp columns show specificity and sensitivity values at each level, while the fSn and fSp columns are "fuzzy" variants of these same accuracy calculations, allowing for a very small variation in exon boundaries to still be counted as a "match". | |
| 186 | |
| 187 Transcripts Combined File: | |
| 188 | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
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189 Cuffcompare reports a GTF file containing the "union" of all transfrags in each sample. If a transfrag is present in both samples, it is thus reported once in the combined gtf. |
| 0 | 190 |
| 191 Transcripts Tracking File: | |
| 192 | |
| 193 This file matches transcripts up between samples. Each row contains a transcript structure that is present in one or more input GTF files. Because the transcripts will generally have different IDs (unless you assembled your RNA-Seq reads against a reference transcriptome), cuffcompare examines the structure of each the transcripts, matching transcripts that agree on the coordinates and order of all of their introns, as well as strand. Matching transcripts are allowed to differ on the length of the first and last exons, since these lengths will naturally vary from sample to sample due to the random nature of sequencing. | |
| 194 If you ran cuffcompare with the -r option, the first and second columns contain the closest matching reference transcript to the one described by each row. | |
| 195 | |
| 196 Here's an example of a line from the tracking file:: | |
| 197 | |
| 6 | 198 TCONS_00000045 XLOC_000023 Tcea|uc007afj.1 j \ |
| 0 | 199 q1:exp.115|exp.115.0|100|3.061355|0.350242|0.350207 \ |
| 200 q2:60hr.292|60hr.292.0|100|4.094084|0.000000|0.000000 | |
| 201 | |
| 202 In this example, a transcript present in the two input files, called exp.115.0 in the first and 60hr.292.0 in the second, doesn't match any reference transcript exactly, but shares exons with uc007afj.1, an isoform of the gene Tcea, as indicated by the class code j. The first three columns are as follows:: | |
| 203 | |
| 204 Column number Column name Example Description | |
| 205 ----------------------------------------------------------------------- | |
| 206 1 Cufflinks transfrag id TCONS_00000045 A unique internal id for the transfrag | |
| 207 2 Cufflinks locus id XLOC_000023 A unique internal id for the locus | |
| 208 3 Reference gene id Tcea The gene_name attribute of the reference GTF record for this transcript, or '-' if no reference transcript overlaps this Cufflinks transcript | |
| 209 4 Reference transcript id uc007afj.1 The transcript_id attribute of the reference GTF record for this transcript, or '-' if no reference transcript overlaps this Cufflinks transcript | |
| 210 5 Class code c The type of match between the Cufflinks transcripts in column 6 and the reference transcript. See class codes | |
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211 |
| 0 | 212 Each of the columns after the fifth have the following format: |
| 213 qJ:gene_id|transcript_id|FMI|FPKM|conf_lo|conf_hi | |
| 214 | |
| 215 A transcript need be present in all samples to be reported in the tracking file. A sample not containing a transcript will have a "-" in its entry in the row for that transcript. | |
| 216 | |
| 217 Class Codes | |
| 218 | |
| 219 If you ran cuffcompare with the -r option, tracking rows will contain the following values. If you did not use -r, the rows will all contain "-" in their class code column:: | |
| 220 | |
| 6 | 221 Priority Code Description |
| 0 | 222 --------------------------------- |
| 6 | 223 1 = Match |
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224 2 c Contained |
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225 3 j New isoform |
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226 4 e A single exon transcript overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment. |
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227 5 i A single exon transcript falling entirely with a reference intron |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffcompare commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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228 6 o Generic exonic overlap with a reference transcript |
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229 7 p Possible polymerase run-on fragment |
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230 8 r Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case |
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231 9 u Unknown, intergenic transcript |
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232 10 x Exonic overlap with reference on the opposite strand |
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233 11 s An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors) |
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234 12 . (.tracking file only, indicates multiple classifications) |
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235 |
| 0 | 236 ------- |
| 237 | |
| 238 **Settings** | |
| 239 | |
| 240 All of the options have a default value. You can change any of them. Most of the options in Cuffcompare have been implemented here. | |
| 241 | |
| 242 ------ | |
| 243 | |
| 244 **Cuffcompare parameter list** | |
| 245 | |
| 246 This is a list of implemented Cuffcompare options:: | |
| 247 | |
| 248 -r An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below. | |
| 249 -R If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts_accuracy file | |
| 250 </help> | |
| 6 | 251 <citations> |
| 252 <citation type="doi">10.1038/nbt.1621</citation> | |
| 253 </citations> | |
| 0 | 254 </tool> |