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Old 10-28-2010, 03:59 AM   #1
Ash
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Location: UK

Join Date: Jun 2010
Posts: 15
Default Finding unmapped reads using samtools

Hi guys,

Samtools is truly amazing! However, there's a couple of things I was wondering about...

Is there any way of pulling out those reads in a bam file, using samtools, where one pair of the read has mapped and the other pair of the read has not?

Or those reads where one pair of the read has mapped and the other mapped in a position that was not expected, say for example 5 or 10kb further upstream?

All help gratefully received!

A
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