Question: Can't we proceed with a SAM file for downstream RNA-Seq data analysis?
0
gravatar for Shaurya Jauhari
2.1 years ago by
China
Shaurya Jauhari40 wrote:

I'm aware that BAM file is easy to handle in terms of disk usage. If hypothetically, I register no shortage of processing power and memory, can I proceed with a SAM file for gene alignment and differential expression analysis? The due course would be different, but what would that be now?

ADD COMMENTlink modified 2.1 years ago by jmzeng131490 • written 2.1 years ago by Shaurya Jauhari40
2

Probably that shouldn't be a problem. But... why would you do that?

ADD REPLYlink written 2.1 years ago by WouterDeCoster40k

This depends on the downstream tools; some may require sorted, indexed bam files. If they don't, though, I'd suggest using sam.gz files; they are typically smaller than bam files and (using pigz) can be processed faster.

ADD REPLYlink written 2.1 years ago by Brian Bushnell16k
0
gravatar for jmzeng1314
2.1 years ago by
jmzeng131490
jmzeng131490 wrote:

sure you can !

but it doesn't make any sense to use the SAM instead of BAM.

Anyway, as you wish .

ADD COMMENTlink written 2.1 years ago by jmzeng131490
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1070 users visited in the last hour