This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Get common segments from several segment files

Hi all! I have a bunch of CNA segment files from multiple samples and want to compare them, problem is all the segments have different start and stop sites in each sample. Is there a one liner pre-built tool to get a new list of segments that covers all the segments from each sample? For example see drawing:enter image description here

copy-number
• 1,299 views • link
updated by Ram Ram • written by heskett • heskett

1 answer

look at bedtools multiinter

 $ bedtools multiinter -header -i a.bed b.bed c.bed -names A B C
 chrom  start   end num list    A   B   C
 chr1   6   8   1   A   1   0   0
 chr1   8   12  2   A,C 1   0   1
 chr1   12  15  3   A,B,C   1   1   1
 chr1   15  20  2   A,B 1   1   0
 chr1   20  22  1   B   0   1   0
 chr1   22  30  2   A,B 1   1   0
 chr1   30  32  1   B   0   1   0
 chr1   32  34  1   C   0   0   1
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Okay I looked into it Pierre. This counts the number of files that have segments at each location, but it doesnt report features at each interval that I am interested in like copy number in this example. But I guess it does give the intervals that I want, so i could then do some kind of bedtools map or bedtools intersect to get the CN values from each file after that. thanks

• 0 views • link
written by heskett • heskett

Log in to answer this question.

More posts like this