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changeset 1:ae06af1118dc

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Update Tophat URLs in help text.
author Nate Coraor <nate@bx.psu.edu>
date Mon, 17 Nov 2014 11:23:41 -0500
parents ffa30bedbee3
children da1f39fe14bc
files tophat2_wrapper.xml
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/tophat2_wrapper.xml	Mon Jan 27 09:26:57 2014 -0500
+++ b/tophat2_wrapper.xml	Mon Nov 17 11:23:41 2014 -0500
@@ -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/
         
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@@ -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
 
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