Ilya Flyamer
Ilya Flyamer
Perhaps cooler should calculate and store cis/total marginals per bin (and cis total counts) at creation time? That would simplify `cooltools random-sample` a lot, and would be useful in general.
Sometimes when balancing is not converging, the variance keeps growing with each iteration. To save time, would it make sense to abort the balancing early in case the variance is...
From what I can tell, the wrapper bwa-memx/index in case of bwa=bwa-meme expects one of the output to be named exactly as {input[0]}.suffixarray_uint64. This file is produced by the first...
If one wants to perform filtering (like > or
And HiC-Spector doesn't work for me either with the following error: ``` Traceback (most recent call last): File "/exports/eddie3_homes_local/s1529682/3DChromatin_ReplicateQC/wrappers/HiC-Spector/run_reproducibility_v1.py", line 209, in main() File "/exports/eddie3_homes_local/s1529682/3DChromatin_ReplicateQC/wrappers/HiC-Spector/run_reproducibility_v1.py", line 202, in main get_reproducibility(M1,M2,int(sys.argv[6]))...
QuASAR-QC always prepends $HOME to the path of the specified folder, i.e. I ran `3DChromatin_ReplicateQC qc --running_mode sge --metadata_samples QCRep_metadata.samples --outdir ./output --methods QuASAR-QC` but it tried to save to...
Hi, thank you for this tool. I just wanted to give it a try, and thought I would suggest you to support input as .cool files - they contain exactly...
Hi, I am trying to run HiCRep using your setup, but can't figure out why I keep getting this error in the .e files (I am running it on the...
Probably would help with docs, which are probably broken... ## Description _Describe what this PR is for_ ## PR Checklist - [] apply "black" to the whole codebase (`black .`)...