Question: Removing Human Reads From Metagenome BAM File
1
gravatar for Kevin.Y
2.3 years ago by
Kevin.Y10
Kevin.Y10 wrote:

So I have metagenome bam files which contain reads for both human and bacteria. I would like to remove all the human reads so I can focus on the bacterial reads. Has anyone been able to remove human reads from their RNA-seq data using samtools or any other software?

rna-seq • 1.3k views
ADD COMMENTlink modified 2.3 years ago by WouterDeCoster37k • written 2.3 years ago by Kevin.Y10

You have it in a bam file, meaning it's already aligned? To what?

ADD REPLYlink written 2.3 years ago by WouterDeCoster37k

It was aligned to a metagenome database for human and bacteria.

ADD REPLYlink written 2.3 years ago by Kevin.Y10
0
gravatar for Tonor
2.3 years ago by
Tonor420
UK
Tonor420 wrote:

Align your reads to the human genome first, then extract all the unmapped reads to work with further. The unmapped reads will have all your bacteria (as well as other non-human things). Extracting unmapped paired end from an alignment - C: Extracting unmapped paired end from an alignment

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Tonor420

This post is useful for removing specific chromosomes from a BAM: Remove mitochondrial reads from BAM files -Remove mitochondrial reads from BAM files

ADD REPLYlink written 2.3 years ago by Tonor420
0
gravatar for WouterDeCoster
2.3 years ago by
Belgium
WouterDeCoster37k wrote:

This sounds like a job for BBsplit

ADD COMMENTlink written 2.3 years ago by WouterDeCoster37k

Agree with @WouterDeCoster, BBSplit can be used, although it is very slow. Here is an example of it Tool to separate human and mouse rna seq reads from one of my posts.

You can probably use seal.sh from BBmap itself which is very fast. The example of Seal.sh is in the above link.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Ron910
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