# HG changeset patch # User Nate Coraor # Date 1416241405 18000 # Node ID 6eaefb5f755acb8ad3126395d96d3e8828f92b1f # Parent 1030acbecce62228ad6b515244c51ee1456a2b01 Update Tophat URLs in help text. diff -r 1030acbecce6 -r 6eaefb5f755a tophat_wrapper.xml --- 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 ------