how extract our desirable data from two table?

Question

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I like to find overlap regions (even with 1 bp) along with the number of counts (fragments) which have overlaps together.

Input:  A.bed

chr1    10  20
chr1    30  50
chr1    35  43
chr1    38  49
chr1    40  50
chr10   15  20
chr10   18  25
chr10   25  30
chr2    20  60
chr2    58  70
chr2    59  75

I have tried a way. First I merged them using bedtools merge and I got the blowing table with the number of regions that have merged.

output1 : column 4 refers to the number of involved fragments in merged coordinates

chr1    10  20  1
chr1    30  50  4
chr10   15  30  3
chr2    20  75  3

Then, using genomeCoverageBed -i A.bed -g hg19.main.chroms.sizes -bga I could get my result but it is among several values:

output2:

chr1    0   10  0
chr1    10  20  1
chr1    20  30  0
chr1    30  35  1
chr1    35  38  2
chr1    38  40  3
chr1    40  43  4
chr1    43  49  3
chr1    49  50  2
chr1    50  249250621   0
chr10   0   15  0
chr10   15  18  1
chr10   18  20  2
chr10   20  30  1
chr10   30  135534747   0
chr2    0   20  0
chr2    20  58  1
chr2    58  59  2
chr2    59  60  3
chr2    60  70  2
 chr2   70  75  1

I like to know how can I link two table together, as the coordinate in output2 should be part of output1, then filter based on column 4 in both data table?

Final output:

chr1    10  20  1       chr1  10  20  1
chr1    30  50  4       chr1  40  43  4
chr2    20  70  3       chr2  59  60  3

Answer 1

[archana.bioinfo87]

Hi,

You can play with bedtools intersect. For more detail can see the below link

https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

Hoping it will help you.