Mercurial > repos > lparsons > htseq_count

diff htseq-count.xml @ 11:f320093f1e8e

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Removed sorting notice from help
author lparsons
date Mon, 10 Dec 2012 13:36:54 -0500
parents 5d969cb56112
children 62a1de8c8aae
line wrap: on
line diff
--- a/htseq-count.xml	Fri Dec 07 14:35:44 2012 -0500
+++ b/htseq-count.xml	Mon Dec 10 13:36:54 2012 -0500
@@ -178,10 +178,6 @@
 comparative ChIP-Seq, the features might be binding regions from a pre-determined 
 list.
 
-**Paired-end Data MUST be sorted by QUERY NAME first**
-
-This tool requires that paired-end data be sorted by query name, which is NOT the default for Galaxy. Using the Picard Paired Read Mate Fixer with Query name sort FIRST is required for paired end data.
-
 
 Overlap Modes
 -------------
@@ -195,11 +191,13 @@
 .. image:: /static/images/count_modes.png
     :width: 500
 
+
 Strandedness
 ------------
 
 **Important**: The default for strandedness is yes. If your RNA-Seq data has not been made with a strand-specific protocol, this causes half of the reads to be lost. Hence, make sure to set the option Stranded to 'No' unless you have strand-specific data!
 
+
 Output
 ------