Mercurial > repos > devteam > tophat

diff tophat_wrapper.xml @ 1:6eaefb5f755a

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update Tophat URLs in help text.
author Nate Coraor <nate@bx.psu.edu>
date Mon, 17 Nov 2014 11:23:25 -0500
parents 1030acbecce6
children 8afd8a379d5f
line wrap: on
line diff
--- a/tophat_wrapper.xml	Mon Jan 27 09:25:27 2014 -0500
+++ b/tophat_wrapper.xml	Mon Nov 17 11:23:25 2014 -0500
@@ -485,7 +485,7 @@
 
 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, and then analyzes the mapping results to identify splice junctions between exons. Please cite: Trapnell, C., Pachter, L. and Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).        
 
-.. _Tophat: http://tophat.cbcb.umd.edu/
+.. _Tophat: http://ccb.jhu.edu/software/tophat/
         
 ------
 
@@ -495,7 +495,7 @@
 
 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
 
 ------