Entering edit mode
8.5 years ago
mbio.kyle
▴
380
Alright biostars, I am on my 4th genome browser (IGV, Savant, Bamview, samscope) and I just can't seem to find anything which works reasonably well. I am on Debian Jessie, running Awesome WM (this is probably part of my problem). I need to compare bam alignments between two different aligners (tophat2 vs RSEM) on hg19.
Anyone have recommendations?
What exactly isn't working in the viewers you've already tried?
Most of the java based applications tend to render very poorly. I have also just ran into alot of issues with getting things up and running (gathering dependencies, building, etc)
Normally one just downloads a .jar, at least with IGV.
I think if you convert your bams into bigWig you will have better luck.
bigWig's are the usual endpoint for me, however I am specifically looking at differences in alignment calls between the two aligners. As such I need to look at the bam level, compare CIGAR strings, etc etc.