Alexander Bender

I would find sending the data to stdout much more useful as this then easily allows to convert to bigwig if one really needs this (e.g. bg2bw from cancerit) as...

Read extension to the average fragment length similar to what `-fs` and/or `-pc` in bedtools genomecov does.

If anyone cares: For me (macOS 10.14.6) the following steps allowed to build mosdepth from scratch: 1. get Nim via https://github.com/dom96/choosenim and follow instructions. Put into PATH (as instructed during...

No, this always returns: ``` $ brew install brewsci/bio/mosdepth ==> Tapping brewsci/bio Cloning into '/usr/local/Homebrew/Library/Taps/brewsci/homebrew-bio'... remote: Enumerating objects: 94, done. remote: Counting objects: 100% (94/94), done. remote: Compressing objects: 100%...

Seems to be working fine. Thanks!

I have a question towards the BAM and BAMPE mode: The TLEN of a pair is of course determined by the insert size after the alignment. I understand that in...

Yes, but I was referring to what happens with paired-end BAMs when not BAMPE but BAM is specified as -f, as this currently seems to be the method of choice...

Yes you are right. The more I think about it, it probably autodetects the bitwise flag for paired-end reads and discards the reverse mate for further analysis.

For recent alternatives have a look at https://github.com/LiuLabUB/HMMRATAC from the Liu lab for ATAC-seq or https://github.com/jsh58/Genrich If you want to use macs and keep both mates you could write the...

> I would say that it's technically right in that the variability is a measure that can be applied to two samples. However, you probably almost certainly have some technical...