igor

Sorry. I am a little confused. I saw a commit that added the ability to read from URL in April 2018: https://github.com/tidyverse/readxl/blob/839d0230832f98fd4f0db38e4a9284983aca0604/R/utils.R#L6-L10 Somehow that edit never got integrated. Was it...

@jennybc Thanks for clarifying. I am just not sure if you are postponing URL handling or giving up on it entirely.

@jennybc Thank you for clarifying again. Dealing with remote data is complicated, so I understand the concern. If my opinion makes any difference, you can add the quick temp file...

Thanks for reporting! Are you using Seurat 4? This may have been one of the changes.

@ATpoint, according to the manual: > Pair-end mapping results can be saved in a single BAM file, if so, MACS will automatically keep the left mate(5' end) tag. However, when...

Based on that description, it sounds like only one mate (left mate) is used when the reads are paired and BAM (not BAMPE) is specified. Essentially, half the reads are...

For anyone still following this discussion (more than 4 years later), there is a related thread on Twitter that brings up some interesting points and suggests using "-f BED --shift...

@taoliu there is now a discussion: https://github.com/macs3-project/MACS/discussions/435 I haven't yet used that GitHub feature, but hopefully it should be more appropriate than an "issue".

Small gene panels is one example, but those are more predictable in this regard. I've also had variable-quality RNA-seq batches where there are some samples that yield few sites. Have...

I tried dbSNP (ftp://ftp.ncbi.nih.gov/snp/organisms/archive/mouse_10090/VCF/00-All.vcf.gz) and EVA RefSNP (ftp://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/release_2/by_species/mus_musculus/GRCm38.p4/GCA_000001635.6_current_ids.vcf.gz). It runs without errors, but also without results: ``` somalier version: 0.2.15 on chrom:1 on chrom:10 on chrom:11 on chrom:12 on chrom:13...