Filter Exon Aligned Reads That Are Mapped Against Human Genome.
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7.1 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 • 2.4k views
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7.1 years ago

duplicate of Samtools and Region List

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

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The online manual is two versions behind.

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

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