Ecc vs non-ecc RNA-seq

[Parharn]

Hi,
Do I need ECC for setting up a workstation for RNA-seq and ChIP-seq analysis? How crucial is that?

Best,
Parham

[dpryan]

No, you don't.

[Parharn]

Would you explain some more? Some people say it is important in downstream analysis, some say not!

[dpryan]

The point of ECC memory is to help guard against memory corruption, primarily when the computations are going to be used in financial transactions or modeling (imagine a case where a bit was flipped early in a weather model, since each time-point is dependent upon the previous state). The question becomes how frequently this actually happens (rarely, though you'll find a huge range of rates being reported) and how big of a problem the results would be. With NGS, you're going to do follow-up validations anyway, so a single value being off is simply not going to have a big effect. There's also the fact that a lot of computers can do the ECC step in CPU, so there's no need for the monetary or performance hit.

Having said that, if it's in your budget then it probably wouldn't hurt. If you're shelling out for a large server (overkill for RNAseq data) then it'll probably already be spec'd for ECC memory, since that's more standard for server-grade hardware.

[ffinkernagel]

ECC guards against bit errors in RAM - these are rare in the first place, and if they occur will most likely just flip one of the bases in your reads - depending on the encoding possibly even to something invalid. What's one read among millions? It will most likely still align to the same place...

ECC is interesting if you need very long running (months) systems where an error must not occur, and you don't have control to work around it in software ( by having data structures with error correction, or triple redudancy for example).

[Parharn]

Thanks people, now my conscious is clear and can decide well!