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Old 02-24-2015, 05:38 AM   #1
Liy
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Location: Hungary

Join Date: Feb 2012
Posts: 19
Smile BWA MEM question

Dear all,

I just have a question about bwa mem alignment. I ran the following simple command:

bwa mem <fa> <fastq> -t 5

Before the alignment I checked the number of reads with fastqc and then after alignment I counted the IDs present in the sam file with grep '<common ID> | wc -l and I got different results.
What causes the difference? Is the multi-mapper reads present in the sam file?

Total reads: 24 961 320
Aligned reads: 24 961 535

Thank you for the answere,
Regards,
Liy
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Old 02-24-2015, 05:48 AM   #2
sarvidsson
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Location: Berlin, Germany

Join Date: Jan 2015
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Default

Run
Code:
samtools view -S -f 0x100 <file.sam>
to get the multimappers.

Last edited by sarvidsson; 02-24-2015 at 05:54 AM. Reason: too quick
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