My apology for reposting my questions. I posted this question last week aan helpnd wonder if some one can help me in this? Thanks
---------- Forwarded message ---------- From: shamsher jagat kanwarjag@gmail.com Date: Wed, Apr 25, 2012 at 7:38 AM Subject: Question about Samtools filter in Galaxy To: galaxy-user galaxy-user@lists.bx.psu.edu Cc: Jennifer Jackson jen@bx.psu.edu
I have a sam file after running BWASW and want to extract unique (alignments that are aligning once to genome) from this sam file. I read in other posts that I may be able to use Sam tools> filter Sam option to filter the said flag on wise flag. However I could not find whether I have to use default setting of column 2? when I use option of add flags there are different options for pair reads, however my data is single reads. So exactly single read alignments sam file how we extract unique reads. Am I missing something. I can also share history in order to explain my point if required.
Thanks
Kanwar