Hello Biostars !!
I have .bed files resulting from Macs peak calling that are biological replicates. I have 5 replicates for healthy people and 6 for patients. I merged the 5 samples to a set for healthy represented in one file and I made the same for the patients so I have one bed file for all the merged peaks from patients and one bed file for healthy.
Now I'm looking for common genomic regions between these two files. I performed an IntersectBed with a UCSC table for the known genes on the genome but I see multiple ways to do the intersectBed :
- intersect condition1 with ucsc table, then intersect condition2 with ucsc and then make a 'super' intersect between the two files obtained ?
- As intersect now allows the use of multiple files, make an intersect between condition1+condition2+ucsc table ?
- Use Venn diagram but here we have the same problem : make a venn diagram 3-points with cond1+cond2+ucsc or make a venn diagram with cond1+ucsc then with cond2+ucsc and compare them ?
Which strategy is the good one ??
Thank you in advance !!