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Old 05-12-2015, 04:24 AM   #14
Michael.Ante
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Location: Vienna

Join Date: Oct 2011
Posts: 123
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You can use samtools view to extract the mapped/unmapped reads by filtering the 'unmapped' flag:

Code:
samtools view -F 4 -bh lib4seq.sorted.bam > lib4seq.sorted.mapped.bam
samtools view -f 4 -bh lib4seq.sorted.bam > lib4seq.sorted.unmapped.bam
Samtools view will help a lot; just have a look at some tutorials, for instance Dave's wiki
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