Question: Genome Browsers with BAM viewing capabilitites - Debian
0
gravatar for mbio.kyle
2.6 years ago by
mbio.kyle290
United States
mbio.kyle290 wrote:

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?

visulization bam • 758 views
ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 2.6 years ago by mbio.kyle290
2

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

ADD REPLYlink written 2.6 years ago by Devon Ryan86k

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)

ADD REPLYlink written 2.6 years ago by mbio.kyle290

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

ADD REPLYlink written 2.6 years ago by Devon Ryan86k

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

ADD REPLYlink written 2.6 years ago by h.mon21k

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.

ADD REPLYlink written 2.6 years ago by mbio.kyle290
1
gravatar for mbio.kyle
2.6 years ago by
mbio.kyle290
United States
mbio.kyle290 wrote:

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

ADD COMMENTlink written 2.6 years ago by mbio.kyle290
1
gravatar for Daniel
2.6 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

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

ADD COMMENTlink written 2.6 years ago by Daniel3.7k

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

ADD REPLYlink written 2.6 years ago by mbio.kyle290
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