Entering edit mode
9 months ago
jkim ▴ 140
This is my bam file in IGV. There are way more reads mapped to the region 2 in the panel displaying reads. On the other hand, the coverage panel shows the opposite - there are more reads mapped to the region 1.
I also ran
samtools depth and it said there are more reads mapped to the region 1. I am confused by this. Did IGV not show me all the reads mapped to the region 1 for some reason? I didn't change any setting for IGV.
may be the IGV algorithm collapsing reads generates a visual bias.
I see. I will post this on the IGV help forum.
perhaps it has something to do with the mapping quality? Image is a bit small but it seems there are much more gaps/indels/mismatches in region2 in stead of 1 ...
perhaps samtools only counts the well mapped reads or such?
Well, I filtered reads out in my bam by mapping quality. Yeah, I will look into
I think I found why. If I unclick
Downsamplingoption in alignment in preferences, it looks like IGV shows every read...