faulk-lab

I'm commenting here in the hopes the authors have a solution to this question. Despite it being 1 year old, this is a problem of growing interest given the explosion...

The reasoning is understandable. The measures I'm most interested in are entropy and partially methylated domains (PMDs). There is currently no method or tool to calculate methylation entropy using native...

For sure! I'd definitely be interested in beta testing. I have lots of relevant bam files that would be a great set of controls for it.

Very excited to try this! Off to a strong start, it appears to be working well, but then I run into a crash. (base) minknow@betsy:~/Desktop/entropy-test$ ../modkit_devel/modkit entropy --ref ~/Desktop/genomes/mouse/mm10.fa ../mouse_bams/mouse_modmapped-mm10/mouse.mm10.modmapped.bam...

This version completes successfully. The num-positions and window-size parameters make perfect sense to me as described. However I don't know what sensible defaults *should* be. I see that DNMTools uses...

One feature request would be a flag to automatically exclude "-0" windows from the output.

Ok, I'm trying this one on a couple of datasets and I'll run it with your specified parameters. I'll let you know how it comes out.

I'm still seeing "-0" even when using the --drop-zeros flag, is that intended behavior?

Feature is working fine, just not a lot interesting scientifically. I've run a few datasets that I expect should have some differences in entropy, yet they all come out extremely...

I'm not sure the `--num-positions` always makes sense in a genomic context at all. For instance, right now I just grabbed the flanking 2000 bp of every CpG island in...