Question: Filter Exon Aligned Reads That Are Mapped Against Human Genome.
0
gravatar for Coryza
5.6 years ago by
Coryza30
Coryza30 wrote:

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?

Thanks1

exon genome mapping hg19 bowtie2 exome • 1.9k views
ADD COMMENTlink written 5.6 years ago by Coryza30
0
gravatar for Pierre Lindenbaum
5.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

duplicate of Samtools and Region List

ADD COMMENTlink written 5.6 years ago by Pierre Lindenbaum123k

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

ADD REPLYlink modified 11 days ago by RamRS24k • written 5.6 years ago by Coryza30

The online manual is two versions behind.

ADD REPLYlink written 5.6 years ago by Devon Ryan92k

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

ADD REPLYlink written 5.6 years ago by Coryza30
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