Question: Remove Intronic Regions in .BAM
0
gravatar for K.Nijbroek
6.7 years ago by
K.Nijbroek100
Netherlands
K.Nijbroek100 wrote:

Hi

I have a .BAM file which contains discordantly and concordantly mapped mate-pairs. I used bedtools Pairtobed to extract the mate-pairs which both show overlap with targeted regions (Illumina target .bed file). Is it somewhere possible to remove the parts of the mate-pairs that do not show overlap? I couldn't find it in the bedtools manual... can I just use intersectBed for each read for this?

 

Thanks!

bam intron exome remove bedtools • 2.1k views
ADD COMMENTlink modified 6.7 years ago by Sukhi Singh10k • written 6.7 years ago by K.Nijbroek100
2
gravatar for Sukhi Singh
6.7 years ago by
Sukhi Singh10k
Netherlands
Sukhi Singh10k wrote:

Once you filter for mate-pairs mapping to targeted regions, the mate-pairs that do not overlap are already removed. If you post an example of what you have and what you want, I can help you more.

With the -type parameter of pairToBed and -v of intersectBed, you can definitely achieve it, but can't pinpoint without a snippet of data.

-type     Approach to reporting overlaps between BEDPE and BED.

    either    Report overlaps if either end of A overlaps B.
        - Default.
    neither    Report A if neither end of A overlaps B.
    both    Report overlaps if both ends of A overlap  B.
    xor    Report overlaps if one and only one end of A overlaps B.
    notboth    Report overlaps if neither end or one and only one 
        end of A overlap B.  That is, xor + neither.

    ispan    Report overlaps between [end1, start2] of A and B.
        - Note: If chrom1 <> chrom2, entry is ignored.

    ospan    Report overlaps between [start1, end2] of A and B.
        - Note: If chrom1 <> chrom2, entry is ignored.

    notispan    Report A if ispan of A doesn't overlap B.
            - Note: If chrom1 <> chrom2, entry is ignored.

    notospan    Report A if ospan of A doesn't overlap B.
            - Note: If chrom1 <> chrom2, entry is ignored.
ADD COMMENTlink modified 13 months ago by _r_am32k • written 6.7 years ago by Sukhi Singh10k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2613 users visited in the last hour
_