Question

Filter Exon Aligned Reads That Are Mapped Against Human Genome.

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10.1 years ago

Coryza ▴ 30

Hi,

I am wondering if it is possible via samtools/bamtools to extract all the paired-end mapped reads (against the human hg19 genome) that fall in exon regions. I have a BED file that defines all these regions. I already know that it's possible to calculate this (coverageBed -abam reads.bam -b exons.bed > exons.bed.coverage), but I have no clue how to extract the reads from the .bam file). I tried using the samtools/bamtools manual but couldn't figure it out.

Anyone who can help me?

Thanks

exons genome mapping hg19 bowtie2 • 3.2k views

ADD COMMENT • link updated 3.1 years ago by Ram 43k • written 10.1 years ago by Coryza ▴ 30

Ram · Answer 1 · 2014-03-27

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10.1 years ago

Pierre Lindenbaum 161k

duplicate of Samtools and Region List

ADD COMMENT • link 10.1 years ago by Pierre Lindenbaum 161k

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Hmm wonder why I could not find that in the samtools manual..

ADD REPLY • link updated 4.5 years ago by Ram 43k • written 10.1 years ago by Coryza ▴ 30

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The online manual is two versions behind.

ADD REPLY • link 10.1 years ago by Devon Ryan 104k

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Ah well, thanks for the help both of you ;)

ADD REPLY • link 10.1 years ago by Coryza ▴ 30