Is there any file format or way to view overlapping coverage or peak values on separate lines or tracks in genome browsers like IGV, and UCSC?
For example in the following figure - - -
I can generate bedgraph or bigwig files from the bam file which may contain genome coverage or some kind of peak signals. Then I can use the file in IGV to view peaks (figure a). This approach shows all signals as a continuous line.
But, based on some criteria I want to group read pairs into different fragments. In that case, some fragments may overlap each other.
Is there any bedgraph like file format where I can store coverage/peak signals with feature names (like fragment 1, fragment 2, etc) and can view peaks of overlapping fragments on separate tracks ( like figure b)
how about generating a bigwig file for each 'criteria' ?
I actually thought about that. The problem is there will be millions of fragments. Generating that many bigwig files is not very preferable.
Well could build a few bigwigs, each with non overlaping bed segments.
Yeah, that can be an option. I wonder if any alternative file format can contain all the info together.
Sounds like maybe you want to visualize the bam directly with maybe a bed file to show boundaries of your features/overlap.
One idea would be to assign the feature name that owns the read to the read as a tag, something like a "read group".
for example if read2/3 overlap, they can be distinguished by the read group. In IGV you can load the bam then color/sort by read group.
Instead of "read group" tag, you may want to use a custom tag and then tell IGV to color by your specific tag.
That can be a good option. Thank you very much for the idea.