Hi, I’m interested in using the MACS2 bdgcmp for my ChIP-seq data that has been quantile normalized outside of MACS2 (linear scaling in MACS is not optimal, quantile normalization validates what I’ve seen with ChIP qPCR and better reflects the biology of the system). Briefly, I calculated genome coverage by measuring read depth in 50bp bins across the genome and then quantile normalized these bins. I then removed all bins with 0 reads. The final data are in bed graph format. I've used the Galaxy based MACS2 bdgcmp with these data, but I get the following error: Exception ZeroDivisionError: 'float division' in 'MACS2.IO.ScoreTrack.get_logFE' ignored
Here is my question: Is it possible to analyze binned genomic coverage data in MACS2?
Any help is greatly appreciated! Ben
