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:

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


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
Am I missing something. I can also share history  in order to explain my
point if required.



Jennifer Jackson
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