Question: Remove Intronic Regions in .BAM
0
gravatar for K.Nijbroek
4.9 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 • 1.7k views
ADD COMMENTlink modified 4.9 years ago by Sukhdeep Singh9.6k • written 4.9 years ago by K.Nijbroek100
2
gravatar for Sukhdeep Singh
4.9 years ago by
Sukhdeep Singh9.6k
Netherlands
Sukhdeep Singh9.6k 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 3.6 years ago • written 4.9 years ago by Sukhdeep Singh9.6k
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