How much memory / how many cores should I request for peak calling?
1
0
Entering edit mode
3.0 years ago
jrleary ▴ 190

I've never run ChIPseq before, so I've been writing a pipeline from scratch to perform all the necessary read trimming, alignment, etc. I've successfully gotten to the peak calling step, which I will be performing using MACS2. My question is, how much memory and how many cores should I request from our HPC cluster for each peak call? I have no idea how computationally intensive the process is, and I'd like it to be completed fairly quickly, while not requesting so many resources that the jobs I submit take forever to get picked up. We use slurm as a job scheduler, if that information makes any difference (doubt it does).

ChIP-Seq slurm • 1.6k views
ADD COMMENT
2
Entering edit mode
3.0 years ago
GenoMax 123k

It will depend on the peak caller you are planning to use. If the peak caller is not thread-aware/multi-threaded you can just ask for a single core. Asking for more cores is not going to speed the process up or allow the program to use multiple cores, if it is not designed/written to do so.

ADD COMMENT
0
Entering edit mode

Ah yes, I had kind of assumed that MACS2 had multithread support but according to this feature request on their GitHub it isn't supported yet. Guess I'll just request one core and a ton of memory. Thanks!

ADD REPLY
1
Entering edit mode

You shouldn't need more than 8 GB of memory for MACS.

ADD REPLY

Login before adding your answer.

Traffic: 1531 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6