Ravi Patel

Hello @r3fang, +1 I get the same error while running the `runChromVar` function: `Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boundaries of non-circular sequence "chrUn_GL456396"`...

@jindalk & @cacaonib, Like I said in my previous message, this error is being generated because some macs2 peaks extend beyond the chromosome lengths. This typically happens for short contigs,...

I removed chrM and all contigs whose names match "_" from individual matrices in R. Below is an example code snippet to remove these chromosomes from a bmat. ``` chr.exclude...

@hjack123 This solution is not exactly what you are looking for, but it comes pretty close, I think. You can use coordinates of promoter regions (e.g. 1kb upstream and 0.5kb...

@JihedC, Can you tell me how you generated your GRanges object? It seems to work for me. I first read my bed intervals into `peaksToGenes` data frame. And then used...

Thanks Jin for a quick reply. The error message in `stderr` file is also present in the .log files (towards the end). Yes, I am running the pipeline locally, with...

I think I found how to post issue on the new repo. Doing that now.

Hi @andrewwbutler, Is there a plan to allow using our own CITE-seq dataset for mapping? Azimuth struggles distinguishing some cell types in our PBMC datasets, in particular, naïve vs memory...