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comparison cufflinks_wrapper.xml @ 1:b9d29fdd1190 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:37:52 -0400
parents 1fffcfe2fb35
children a6f581469476
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0:1fffcfe2fb35 1:b9d29fdd1190
212 <help> 212 <help>
213 **Cufflinks Overview** 213 **Cufflinks Overview**
214 214
215 Cufflinks_ assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. 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 215 Cufflinks_ assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. 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
216 216
217 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ 217 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
218 218
219 ------ 219 ------
220 220
221 **Know what you are doing** 221 **Know what you are doing**
222 222
223 .. class:: warningmark 223 .. class:: warningmark
224 224
225 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. 225 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.
226 226
227 .. __: http://cufflinks.cbcb.umd.edu/manual.html 227 .. __: http://cole-trapnell-lab.github.io/cufflinks/cufflinks/
228 228
229 ------ 229 ------
230 230
231 **Input formats** 231 **Input formats**
232 232