I used bwa to align a short read file to a reference sequence. I ran it several times, and I got different results for the runs on the same input dataset. The fist run, it generated a ~280,000 lines "gzipped file". I checked the file on the server, and it was actually a sam file, not gzipped. The second run, it generated ~90,000 lines sam file. The third run, it generated ~130,000 lines sam file. The fourth run, it generated ~220,000 lines "gzipped file"
Does anyone meet the similar problem? Thank you very much. Cai ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
