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comparison cuffcompare_wrapper.xml @ 1:6d8ab54229a0 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:37:24 -0400
parents d0d26169cc2a
children a5674ddf2ad7
comparison
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0:d0d26169cc2a 1:6d8ab54229a0
153 <help> 153 <help>
154 **Cuffcompare Overview** 154 **Cuffcompare Overview**
155 155
156 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 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
157 157
158 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ 158 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
159 159
160 ------ 160 ------
161 161
162 **Know what you are doing** 162 **Know what you are doing**
163 163
164 .. class:: warningmark 164 .. class:: warningmark
165 165
166 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 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.
167 167
168 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffcompare 168 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/
169 169
170 ------ 170 ------
171 171
172 **Input format** 172 **Input format**
173 173
223 --------------------------------- 223 ---------------------------------
224 1 = Match 224 1 = Match
225 2 c Contained 225 2 c Contained
226 3 j New isoform 226 3 j New isoform
227 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. 227 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.
228 5 i A single exon transcript falling entirely with a reference intron 228 5 i A single exon transcript falling entirely with a reference intron
229 6 r Repeat. Currently determined by looking at the reference sequence and applied to transcripts where at least 50% of the bases are lower case 229 6 o Generic exonic overlap with a reference transcript
230 7 p Possible polymerase run-on fragment 230 7 p Possible polymerase run-on fragment
231 8 u Unknown, intergenic transcript 231 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
232 9 o Unknown, generic overlap with reference 232 9 u Unknown, intergenic transcript
233 10 . (.tracking file only, indicates multiple classifications) 233 10 x Exonic overlap with reference on the opposite strand
234 11 s An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)
235 12 . (.tracking file only, indicates multiple classifications)
234 236
235 ------- 237 -------
236 238
237 **Settings** 239 **Settings**
238 240