Question: Removing Unmapped Reads from SAM File (SAMTools)
0
gravatar for gtasource
6 weeks ago by
gtasource30
gtasource30 wrote:

I know, this question is everywhere. But I have yet to see somebody use the same samotols command as myself, and I wanted to double-check.

samtools view -S -f 4 aligned.sam > unmapped.sam

Yay?

samtools • 105 views
ADD COMMENTlink modified 6 weeks ago by swbarnes27.0k • written 6 weeks ago by gtasource30

Try it. If reads with a * in chromosome field are gone then you are all set.

ADD REPLYlink written 6 weeks ago by genomax75k

Just to clarify, the * in the chromosome signifies unmapped reads? So, in the above command, since I am extracting unmapped reads into a separate file, that file should have mostly reads with * in the chr field.

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by gtasource30
0
gravatar for swbarnes2
6 weeks ago by
swbarnes27.0k
United States
swbarnes27.0k wrote:

Your way is fine. The -S is optional; the default behavior of samtools view is to output as sam, not bam.

ADD COMMENTlink written 6 weeks ago by swbarnes27.0k
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