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comparison cuffquant_wrapper.xml @ 1:8fb10700729b draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:38:32 -0400
parents cef77c81d60c
children 6c7e4034e354
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0:cef77c81d60c 1:8fb10700729b
161 <help> 161 <help>
162 **Cuffquant Overview** 162 **Cuffquant Overview**
163 163
164 Cuffquant is part of Cufflinks_. Cuffquant provides pre-calculation of gene expression levels. The resulting file can be provided to cuffdiff or cuffnorm for further processing. 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 164 Cuffquant is part of Cufflinks_. Cuffquant provides pre-calculation of gene expression levels. The resulting file can be provided to cuffdiff or cuffnorm for further processing. 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
165 165
166 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ 166 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
167 167
168 ------ 168 ------
169 169
170 **Know what you are doing** 170 **Know what you are doing**
171 171
172 .. class:: warningmark 172 .. class:: warningmark
173 173
174 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. 174 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.
175 175
176 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff 176 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffquant/
177 177
178 ------ 178 ------
179 179
180 **Input format** 180 **Input format**
181 181