dankoc / grohmm Goto Github PK

Hi! I'm currently working on a nascent analysis pipeline (which you can find here) which utilizes GroHMM in its analysis. We are currently working to put together a set of parameters (LTProbb and UTS) to use for the tuning step automatically - is there a list of parameters recommended for general use case? Currently we plan to tune with this set of parameters but we were hoping for a more time-optimized list of tuning parameters.
We hope to hear from you soon!

Hello -- running your tutorial with my own bam files I got this error at detectTranscripts:

Error in Fp[[i]] + 1 : non-numeric argument to binary operator

The fix was to run keepStandardChromosomes to remove any unusual seq levels from the granges object. This could also be achieved with just dropping empty seq levels probably.

Also detectTranscripts caused a segfault in Rstudio -- I think it was just too much text printing to the console.

Looks like mc.cores is automatically set to 10 not the value of the argument?