We have some Chip-Seq data (from Human HeLa cells, 30 million reads) for our factor of interest. If I check my data on a genome browser at some of my peaks called by MACS, I can not see anything in the BigWig (this is totally empty) while I can clearly see the BAMs (they are enriched where there is a peak). Most peaks are OK, BAMs and BigWig show the peak. But I have this problem of empty BigWig for some of these peaks.
I thought BigWig was just a sort of "better" representaiton of BAMs density. Is there some sort of filter when converting from BAMs to BigWig that could explain this discrepancy?
thank you for your help, Xavier