How to remove reads associated with a specific region from bam file?

Question: How to remove reads associated with a specific region from bam file?

5.7 years ago by

United States

Dear Members,

Is there a way I can removes reads associated with a region (chr, start, end) from a .bam file (RNASeq data) prior to the application of HTSeq?

I will greatly appreciate your feedback,

Noushin

rna-seq samtools alignment • 6.4k views

ADD COMMENT • link •

modified 4.2 years ago by Ron • 1.0k • written 5.7 years ago by noushin.farnoud • 110

4.2 years ago by

Sergey Naumenko • 380

Sergey Naumenko • 380 wrote:

bedtools intersect -abam file.bam -b filter.bed -v > filtered.bam

filter.bed should contain

chr    start     end

ADD COMMENT • link written 4.2 years ago by Sergey Naumenko • 380

Thats perfect solutions !! Super cool ! thanks !!!

ADD REPLY • link written 4.0 years ago by abaluapuri • 0

5.7 years ago by

John ♦ 12k

Germany

John ♦ 12k wrote:

You'll want to use NGSUtil's bamutils tool, specifically with -excludebed.

But, id recommend you dont :P
The BAM format is to store highly compressed alignment data. You should treat them like raw, virgin data, without normalization/filtering tweaks here and there to get it into shape.
All that kind of intersection stuff should be done on processed signal data - wigs and bedgraphs, etc - where its much easier to have multiple versions of things and to just dump it all and start afresh from the .bam if you have to.

Having said that, its your data, do what you like with it :)

ADD COMMENT • link modified 5.7 years ago • written 5.7 years ago by John ♦ 12k

4.7 years ago by

sunhanice • 230

United States

sunhanice • 230 wrote:

Just found, there is an option -U in samtools view. Use it like this:

samtools view input.bam -b -h -o output_inRegions.bam -U output_outRegions.bam -L Regions.bed

ADD COMMENT • link written 4.7 years ago by sunhanice • 230

Just to clarify, I used - samtools view in.sorted.bam -b -h -o inRegions.bam -U outRegions.bam "chr:start-stop"... So here the -o file excludes the regions "chr:start-stop" and has the rest, but the -U file only retains the "chr:start-stop"? Thank you for your help!

ADD REPLY • link modified 4.0 years ago • written 4.0 years ago by varsha619 • 90

4.7 years ago by

igor ♦ 12k

United States

igor ♦ 12k wrote:

If you are filtering your BAM for HTSeq, then you are doing extra work. You should just modify the GTF file that you are giving to HTSeq to exclude regions you do not want.

ADD COMMENT • link written 4.7 years ago by igor ♦ 12k

4.2 years ago by

Ron • 1.0k

United States

Ron • 1.0k wrote:

Using this QC package for RNAseq http://rseqc.sourceforge.net

Split_bam.py would do the splitting of bam files.

ADD COMMENT • link written 4.2 years ago by Ron • 1.0k

Please log in to add an answer.

Similar posts • Search »