I am trying to view a few ATACseq and Chipseq bigwig files in UCSC. I have identified the peaks for each file, converted them to bigwig, and was able to upload them and see them in UCSC genome browser. However, what I see in
full mode is a bunch of vertical lines:
I have also converted one of the bigwigs to wig, and the head shows as
#bedGraph section chr1:4768516-52764353 chr1 4768516 4768642 1 chr1 4769922 4770097 1 chr1 4780151 4780361 1 chr1 4785434 4786005 1
This is because every read is being plotted, so the Y axis goes between 0 and 1. I.e., there is no windowing happening. So here I have a few questions
- I'm wondering how I can specify the windows? In UCSC, the window is given with mean+whiskers, max, etc., so it will always show
1as the end result. But shouldn't it be computing the coverage in a given range?
- Should I compute the coverage myself in a
.bedgraph, convert to
.bw, and then upload?
- Is the windowing done on the bigwigs, or is it done in the UCSC genomebrowser?
- Am I making any mistake or misunderstanding anything?