Zepeng (Phoenix) Mu

I noticed the same thing. Basically change qvalue cutoff does not alter the number of peaks in output. I'm wondering how to solve this?

I just figured this out, thanks!

I think k-mer length must be smaller than read length?

Hi @rcorces, I can confirm this behavior is reproducible using tutorial data. ```r library(ArchR) inputFiles

Hi, I'm wondering whether this is because of some stochasticity in Seurat `TransferData` and it is run twice to get `cellGroup` and `cellName`? https://github.com/GreenleafLab/ArchR/blob/968e4421ce7187a8ac7ea1cf6077412126876d5f/R/RNAIntegration.R#L472-L479

Turned out that one of my input files is missing, and snakemake does not through an error. When I deleted the output of that rule, snakemake did through an error,...

Thanks for the quick reply. I actually also need set `build=F`. I'm not sure what it means. My R is installed with conda. It worked fine before, but I recently...

Sounds great! I would like to try the newer version with fewer dependencies when it's available.

Hello, I'm trying to use the new 1.0.3 version to prepare HLA reference. I found that many GRCh38 files from 1000G has no counterpart in GRCh37, or is very hard...

Solved this by making a separate Conda environment for everything. There are several warnings in `cmake` but everything is fine. I think the reason is the difference between GNU 4.8.5...