Can't we proceed with a SAM file for downstream RNA-Seq data analysis?

Question

[Shaurya Jauhari]

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?

[WouterDeCoster]

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

[Brian Bushnell]

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.

Answer 1

[jmzeng1314]

sure you can !

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

Anyway, as you wish .