ChristopherWilks

Hi @tewengtong, The Snaptron (the service) adds the prefix of the compilation to each row on return (e.g. in this case "srav2"). That said, the backing data file, https://snaptron.cs.jhu.edu/data/srav2/junctions.bgz *only*...

Hi @mayank-singh-sikarwar, Thanks for the detailed bug report. I've uploaded the latest (fixed) docker image for 1.2.0 to the public docker repo. I can't specifically speak to the other repo...

(also, note the `--no-auc-stdout --no-annotation-stdout --no-coverage-stdout --gzip` in my command, those will 1) force auc, annotation coverage, and base coverage to files rather than standard out (default) as well as...

actually, I can see there is one or more bugs around the non-bigwig base-level coverage output, at least when `--min-unique-qual 10` is specified. Let me look into fixing that.

Hi @mayank-singh-sikarwar, Thanks for the followup, good to know your goals with using megadepth (and monorail/recount3). I'll have to look into running megadepth via the docker container question as I'm...

Hi @AlexWeinreb, thanks for the feedback (and for using Megadepth). You are correct in both points. I went back and looked at what I'm doing and it's reasonable to think...

Hi @AlexWeinreb I've created a minor pre-release which should now support the XS:A tag in BAM files if present. Please give it a try out and let me know if...

@AlexWeinreb I just made a minor adjustment to the 1.1.2 prerelease with support for the XS:A tag, it's now: https://github.com/ChristopherWilks/megadepth/releases/tag/1.1.2a

Hi @lmanchon, While Megadepth doesn't have that specific capability in terms of output (and it doesn't operation on BED files as the source of reads), if you have a BAM...

Hi @jeskowagner, Thanks for the interest in Megadepth. I think I'd need to hear a bit more about your use case for the proposed BigWig feature. While I'm open to...