X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=blobdiff_plain;f=convert_sam_for_rsem;h=a6bc1248c5881738a1d4862e47deb446c5f3c865;hp=ee035f0ff471b62515ffd173cdea161fe488c521;hb=4a435fbee229af1dd5f76b4feb0ca71398ac8796;hpb=28196eb2a94c1585850189028fcaf7d51fbf68b8

diff --git a/convert_sam_for_rsem b/convert_sam_for_rsem
index ee035f0..a6bc124 100755
--- a/convert_sam_for_rsem
+++ b/convert_sam_for_rsem
@@ -165,7 +165,9 @@ 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.
+Note: You do not need to run this script if Bowtie (not Bowtie 2) is used, or the order of @SQ lines is the same as 'reference_name.idx.fa' and the alignment lines of a same read group together and the mates of the same alignment are adjacent each other for paired-end reads.
+
+Note: This program can only recognize SAM files. See ARGUMENTS section.
 
 =head1 EXAMPLES