Hardware requirements for HTSeq count and DESeq2

[LauGP]

Hello everyone,

I´m willing to analyze RNA-Seq Tophat output data in this pipeline HTSeq count/DESeq2. I also read from previews threads that HTSeq count is designed for little RAM. I´m working in a modest Core 2 Duo 2.4 GHz with 2 Gb of RAM, is this enough for what I´m planning to do? Are there any specific hardware requirements for HTSeq count and DESeq2?

Regards

[dpryan]

That's probably sufficient (the only way to know for sure is to try). The only caveat will be if you have a LOT of samples, then I suppose DESeq2 could try to use all of the memory.

[LauGP]

Thanks for your fast answer!
I have 18 samples, could I consider that as a lot?

[dpryan]

No, a lot would be hundreds (e.g., if you were doing a large clinical experiment). I just tried a similar sized experiment and needed a few hundred megs of memory, so you shouldn't have issues.

[LauGP]

No, a lot would be hundreds (e.g., if you were doing a large clinical experiment). I just tried a similar sized experiment and needed a few hundred megs of memory, so you shouldn't have issues.

Great!
Thanks a lot, I will try then very soon