how to merge peaks when finished IDR consistency test in ATAC-seq data?
hi, I have 3 biological replicates of ATAC-seq data, named a,b,c. I want to find some consistent peaks among these replicates. And I apply idr ---compare ab,ac,bc respectively. Thus, I get three bed files, but I don't know how to merge these files to get a consistent peak file of 3 replicates. Could you help me solve this problem? Thanks a lot!
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How about
bedtools merge? Or use a peak caller that takes replicates right away such asGenrich.DiffBind(Bioconductor package) has some functions to merge peaks as well.I got bedfiles from idr software. I want to merge these consistent peaks but not the original peaks. bedtools merge may not help....
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I do not quite follow. So you should have three peak lists, one from each sample, and you ran IDR 3 times, right, so comparing ab, bc, ac, is that correct? That should give you three "IDR" lists. Now you could merge them with
bedtools mergelike:Does that make sense here?
hi,I had the same problem,did you already have a solution?Looking forward to your reply!Thanks a lot!