Jake

Q: atac-seq nolambda?

2

Hi, I have seen most papers doing ATAC-Seq analysis run macs2 with the --nolambda option, including the hmmratac paper. Naively, it seems like this would overcall peaks/peak summits in generally...

I am trying to generate a set of consensus peaks from a number of ATAC-Seq samples. A number of papers pool all of the samples and call peaks on the...

high memory usage killing job

1

**Describe the bug** Hi, I am trying to run crispressoPooled on a fastq file with 50 million reads and the job keeps getting killed for high memory usage. I gave...

Quantile cutoffs in UMAP plots

4

Hi, Both Seurat and Scanpy have a feature to pass a quantile cutoff when plotting gene expression on a UMAP. I was wondering if it would be possible to request...

Segmentation fault sambamba

2

Hi, I am trying to run the pipeline on some files from encode. I keep getting a segmentation fault killing the job when running sambamba to sort the files. However,...