I am computing irreproducible discovery rate (see here https://sites.google.com/site/anshulkundaje/projects/idr ) for my two ChIP seq profiles for Pol II on same cell line.
My peaks were called using MACS2 and peaks for both ChIP seq profiles were of width 500-520 bases.
I am using following command to compute IDR:
Rscript batch-consistency-analysis2.r ./encodepeaks_1 ./encodepeaks_2 -1 ./Analysis 0 F p.value
If you have used this IDR package you must be knowing that you get a file which has genomic co-ordinates from two ChIP seq profiles which are overlapping with a IDR value in last column (lower the IDR, better the peak).
My problem is few of the genomic co-ordinate in the resulting file are much bigger, in the range of 20041463 bps. Which is very abnormal because none of my peaks are that broad in any of the profile original profile (given as input, i.e., broadpeak1 & broadpeak2).
Have you ever faced such a problem while using IDR? if yes, how you had solved it? I cannot discard these peaks because they fall on my target gene, but they are just too broad.
Please give your advice or suggestion or solution.