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comparison cuffmerge_wrapper.xml @ 1:02f427c3614b draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:38:05 -0400
parents e556721b9872
children 0ed8b7f6d506
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0:e556721b9872 1:02f427c3614b
95 <help> 95 <help>
96 **Cuffmerge Overview** 96 **Cuffmerge Overview**
97 97
98 Cuffmerge is part of Cufflinks_. 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 98 Cuffmerge is part of Cufflinks_. 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
99 99
100 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ 100 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
101 101
102 ------ 102 ------
103 103
104 **Know what you are doing** 104 **Know what you are doing**
105 105
106 .. class:: warningmark 106 .. class:: warningmark
107 107
108 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. 108 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.
109 109
110 .. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge 110 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/
111 111
112 ------ 112 ------
113 113
114 **Input format** 114 **Input format**
115 115