From: Bo Li Date: Fri, 9 Dec 2011 23:57:17 +0000 (-0600) Subject: convert-sam-for-rsem is updated X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=49b0c7bb83c65eb04888c738fef29354bbd1ce12 convert-sam-for-rsem is updated --- diff --git a/convert_sam_for_rsem b/convert_sam_for_rsem index 9bdd033..ee035f0 100755 --- 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'.