Entering edit mode
3.0 years ago
rohitsatyam102 ▴ 690
I have 142 .bed files related to various cell types that are in standard bed format and contains coordinates. I have been recently tasked to figure out which regions are common in at least 10 cell types. I am perplexed about how to achieve that. Because let's say if we intersect a bed file with 10 different bed files and say 9th bed file has altogether different coordinates while rest of the files have highly overlapping regions, such regions won't come up because those regions are absent from 9th bed file.
Maybe you could tackle this task by generating a huge bed file with all coordinates stated in your 142 bed files. And then go from there? Maybe intersecting the huge file with all 142, if thats possible?
bedtools multiintermeant to be used for this? Why does it have to be 10?
My boss asked me to take "at least 10" criteria. Bedtools multiintersect does help but how to fulfil at least criteria?