Genome Browsers with BAM viewing capabilitites - Debian

Question

[mbio.kyle]

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?

[Devon Ryan]

What exactly isn't working in the viewers you've already tried?

[mbio.kyle]

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)

[Devon Ryan]

Normally one just downloads a .jar, at least with IGV.

[h.mon]

I think if you convert your bams into bigWig you will have better luck.

[mbio.kyle]

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.

Answer 1

[mbio.kyle]

So far http://goldenhelix.com/products/GenomeBrowse/ is winning.

Answer 2

[Daniel]

I recently found out about ReadXplorer, and find it particularly good for reading in BAMs, then it stores everything in a db for quick retrieval.

https://www.uni-giessen.de/fbz/fb08/Inst/bioinformatik/software/ReadXplorer

http://bioinformatics.oxfordjournals.org/content/30/16/2247

[mbio.kyle]

I will have a look at this. Thanks very much.