| Previous changeset 0:ffa30bedbee3 (2014-01-27) Next changeset 2:da1f39fe14bc (2014-12-18) |
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Commit message:
Update Tophat URLs in help text. |
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modified:
tophat2_wrapper.xml |
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| diff -r ffa30bedbee3 -r ae06af1118dc tophat2_wrapper.xml --- a/tophat2_wrapper.xml Mon Jan 27 09:26:57 2014 -0500 +++ b/tophat2_wrapper.xml Mon Nov 17 11:23:41 2014 -0500 |
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| @@ -455,7 +455,7 @@ TopHat_ is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie(2), and then analyzes the mapping results to identify splice junctions between exons. Please cite: Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, and Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36, 2013. -.. _Tophat: http://tophat.cbcb.umd.edu/ +.. _Tophat: http://ccb.jhu.edu/software/tophat/ ------ @@ -465,7 +465,7 @@ There is no such thing (yet) as an automated gearshift in splice junction identification. 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. -.. __: http://tophat.cbcb.umd.edu/manual.html +.. __: http://ccb.jhu.edu/software/tophat/manual.shtml ------ |