# HG changeset patch
# User fubar
# Date 1376299087 14400
# Node ID 94c94e25d61ccf11a81bb9cdf0e7894fa5db920f
# Parent  1ce3d6f45fbc595794364c6368bae2da2ad56c04
Uploaded

diff -r 1ce3d6f45fbc -r 94c94e25d61c rgrnastar/rg_rnaStar.xml
--- a/rgrnastar/rg_rnaStar.xml	Mon Aug 12 05:07:28 2013 -0400
+++ b/rgrnastar/rg_rnaStar.xml	Mon Aug 12 05:18:07 2013 -0400
@@ -245,14 +245,17 @@
 strand (i.e. containing only non-canonical junctions) will be suppressed.
 
 If you have stranded RNA-seq data, you do not need to use any specific STAR options. Instead, you need
-to run Cufflinks with the library option --library-type options. For example, cufflinks <...> -
-library-type fr-firststrand should be used for the “standard” dUTP protocol. This option has
-to be used only for Cufflinks runs and not for STAR runs.
+to run Cufflinks with the library option --library-type options. For example, cufflinks with
+library-type fr-firststrand should be used for the “standard” dUTP protocol.
+This option has to be used only for Cufflinks runs and not for STAR runs.
 
 It is recommended to remove the non-canonical junctions for Cufflinks runs using –
+
 --outFilterIntronMotifs RemoveNoncanonical
 filter out alignments that contain non-canonical junctions
+
 OR
+
 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
 filter out alignments that contain non-canonical unannotated junctions
 when using annotated splice junctions database. The annotated non-