# HG changeset patch
# User lparsons
# Date 1355164614 18000
# Node ID f320093f1e8e6a480ca4625dab16edc05fed5d3b
# Parent  5d969cb56112172cf57c7a9d736f26073be499df
Removed sorting notice from help

diff -r 5d969cb56112 -r f320093f1e8e htseq-count.xml
--- 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
 ------