Question: Can't we proceed with a SAM file for downstream RNA-Seq data analysis?
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gravatar for Shaurya Jauhari
19 months 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 19 months ago by jmzeng131490 • written 19 months ago by Shaurya Jauhari40
2

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

ADD REPLYlink written 19 months ago by WouterDeCoster36k

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 19 months ago by Brian Bushnell16k
0
gravatar for jmzeng1314
19 months 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 19 months ago by jmzeng131490
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