convert-sam-for-rsem is updated

diff --git a/convert_sam_for_rsem b/convert_sam_for_rsem
index 9bdd0336baf18c33a318fe3153d41f67277d7eac..ee035f0ff471b62515ffd173cdea161fe488c521 100755 (executable)
--- a/convert_sam_for_rsem
+++ b/convert_sam_for_rsem
@@ -165,6 +165,8 @@ Show help information.
 
 This program converts the SAM file generated by user's aligner into a SAM file which RSEM can process. However, users should make sure their aligners use 'reference_name.idx.fa' generated by 'rsem-prepare-reference' as their references. In addition, their aligners should output header information and make two mates of the same alignment adjacent to each other for paired-end data. This program will output the converted file into standard output by default for the purpose of piping. By setting '-o' option, users can make the converted file written into disk.
 
+Note: You do not need to run this script if Bowtie (not Bowtie 2) is used.
+
 =head1 EXAMPLES
 
 Suppose reference_name and input_sam are set to '/ref/mouse_125' and 'input.sam'.