Carlos Guzman

The problem appears to be fixed by increasing the End coordinate by 1 if that helps.

Silly mistake, great catch! Will update this today, and you're completely right. The genome for those datasets are human. Will update that information. On Jan 20, 2018 5:15 AM, "Bioninbo"...

Are you setting up your config.txt file correctly? You mentioned you're using PBS right? So your config file should be set up to submit PBS jobs, and then you just...

Hmm. I'm not entirely familiar with running CIPHER on a PBS cluster. I've mainly used SLURM and it worked fine. I don't think setting the cpus directive will solve the...

Ahh, I misunderstood. Sure, to use multiple cpus per process just make sure to add the --threads parameter to your nextflow script .... such as nextflow run cipher.nf --mode ........

If that's the case then please try adding the cpus directive to your nextflow.config ... if that fixes the issue let me know On Oct 16, 2017 12:02 AM, "shen"...

Yes, I was hoping that specifying the cpu in the config file would go around this, i'll go ahead and edit the cipher script sometime today and get this to...

I just wanted to leave a comment here to encourage that this sort of feature be looked into. Would be super awesome to use this for DNase-seq and ATAC-seq datasets....

Any update on this @smolkmo?

Was wondering if there have been any updates for bench-marking RNA-seq aligners?