faulk-lab

Use bam files with MM and ML tags with native 5mC calls, no bisulfite conversion.

1

metheor looks like exactly the tool I need, however I am not using bisulfite data as input. I called methylation directly using nanopore sequencing and my .bam files store it...

Convert bam to pseudo bisulfite output

37

Is there a way to convert a modified mapped or unmapped bam containing the MM/ML tags into a pseudo bisulfite output? In other words, convert every unmodified C to T...

Add additional reporting outputs like nanoq does, so you could have full report, or 1-line version, or more. This would help when running cramino in a script to generate output...

--call-mods not working on m6a

5

I'm trying to filter a bam to clamp mod-A to either 0 (canonical) or 100 (modified) so that I can view it in Jbrowse2 showing similar percentages as I am...

Add additional measures of heterogeneity / entropy

1

Could you add some additional measures of read heterogeneity ala "[metheor](https://github.com/dohlee/metheor)"? I'm in most need of Proportion of discordant reads (PDR), as it is a measure of epigenetic erosion. The...

Ragtag scaffold inserted a uracil.

1

Very strange error. I ran `ragtag scaffold` using a published genome (GWHETLT00000000.1) and my own assembly. Neither assembly has any "U" bases within them. Somehow, ragtag scaffold generated a Uracil...

samtools.org security issue?

4

I googled 'samtools download' and was presented with a website "samtools.org" that looks for all the world like a malware distribution site. The insane graph they have is *clearly* AI...