Question About Samtools Filter In Galaxy

Question: Question About Samtools Filter In Galaxy

6.6 years ago by

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shamsher jagat • 590 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

bwa alignment • 1.6k views

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modified 6.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.6 years ago by shamsher jagat • 590

6.6 years ago by

shamsher jagat • 590

United States

shamsher jagat • 590 wrote:

My apology for reposting my questions. I posted this question last week aan helpnd wonder if some one can help me in this? Thanks 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

ADD COMMENT • link written 6.6 years ago by shamsher jagat • 590

6.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.6 years ago by Jennifer Hillman Jackson ♦ 25k

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