Hi Kanwar,

A simple way is to just treat the SAM dataset as a text file and perform some counts similar to those in this tutorial:
https://main.g2.bx.psu.edu/u/aun1/p/galaxy101

The basic outline would be to:
1 - remove unmapped with Filter SAM, "The read is unmapped", "no"
2 - convert sam -> interval
3 - group on column 1 (the sequence identifier), then count distinct
4 - select lines with a count of "1"
5 - join back those identifiers with the original sam to extract the alignments

Thanks!

Jen
Galaxy team

On 4/25/12 7:38 AM, shamsher jagat wrote:
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


--
Jennifer Jackson
http://galaxyproject.org
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