Question: How to remove reads associated with a specific region from bam file?
2
gravatar for noushin.farnoud
3.4 years ago by
United States
noushin.farnoud90 wrote:

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 • 3.2k views
ADD COMMENTlink modified 23 months ago by Ron820 • written 3.4 years ago by noushin.farnoud90
5
gravatar for Sergey Naumenko
23 months ago by
Sergey Naumenko330 wrote:
bedtools intersect -abam file.bam -b filter.bed -v > filtered.bam

filter.bed should contain

chr    start     end
ADD COMMENTlink written 23 months ago by Sergey Naumenko330

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

ADD REPLYlink written 20 months ago by abaluapuri0
4
gravatar for John
3.4 years ago by
John12k
Germany
John12k 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 COMMENTlink modified 3.4 years ago • written 3.4 years ago by John12k
3
gravatar for sunhanice
2.5 years ago by
sunhanice190
United States
sunhanice190 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 COMMENTlink written 2.5 years ago by sunhanice190
1

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 REPLYlink modified 20 months ago • written 20 months ago by varsha61970
3
gravatar for igor
2.5 years ago by
igor6.8k
United States
igor6.8k 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 COMMENTlink written 2.5 years ago by igor6.8k
2
gravatar for Ron
23 months ago by
Ron820
United States
Ron820 wrote:

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

Split_bam.py would do the splitting of bam files.

ADD COMMENTlink written 23 months ago by Ron820
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