Hi,
I have two replicates for five histone marks (three of them are broad chromatin marks). I would like to retrieve the overlapping peaks for the replicates for further analysis.
I tried calling peaks with macs2 for the replicates separately as well as by combining them. Since the peaks from the merged replicates would probably be skewed, I tried DiffBind (dba.overlap) with the separately called peaks. I was able to obtain the numbers of overlapped peaks for the replicates in a Venn diagram, but I failed to find how to write the overlapped peaks into a bed file.
Another suggestion I came across while trying to find another solution was IDR analysis, but I guess it is not recommended for broad chromatin.
Can someone tell me how to write the overlapping peaks from DiffBind to a file? Or any other suggestion would also be appreciated.
I have two replicates for five histone marks (three of them are broad chromatin marks). I would like to retrieve the overlapping peaks for the replicates for further analysis.
I tried calling peaks with macs2 for the replicates separately as well as by combining them. Since the peaks from the merged replicates would probably be skewed, I tried DiffBind (dba.overlap) with the separately called peaks. I was able to obtain the numbers of overlapped peaks for the replicates in a Venn diagram, but I failed to find how to write the overlapped peaks into a bed file.
Another suggestion I came across while trying to find another solution was IDR analysis, but I guess it is not recommended for broad chromatin.
Can someone tell me how to write the overlapping peaks from DiffBind to a file? Or any other suggestion would also be appreciated.
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