Arthur Rand
Arthur Rand
Hello @kir1to455, Thanks, could you check one more thing for me. In the `extract` and `pileup` logs there should be some log lines that describe how the sampling they should...
Hello @kir1to455, Sorry for the delayed response. The thresholds are ending up different because in `modkit extract` the pass threshold is estimated at only the third position `DRACH` motifs (the...
Hello @kir1to455, The extract tables can get rather large and buffering them in memory as you've discovered can balloon. Here are three things to try: 1. Reduce the argument to...
Hello @setshabaTaukobong, What I would do is run `modkit dmr pair` with `--regions ${bed_file}` where the `bed_file` contains your introns, exons, promoters, TSS, etc. You can find some instructions for...
Hello @lucy924, Could you send me the whole panic message?
Hello @lucy924, thanks for sending the traceback. I'll have a build to you with the fix asap.
Hello @lucy924, What you're doing looks reasonable to me. With respect to this error: ```text > sampled 46 a records and 0 b records, calculating max coverages for 95th percentile...
Hello @lucy924, Thanks for sending the logs over. Do other chromosomes 6mA DMR seem to work and just chr14 is having problems? One thing I noticed is that you use...
Hello @lucy924, I've made a refactor to how the tabix indices are handled in `dmr`. Please find a build attached. Hopefully with this build the outputs from the various runs...
This fix has been merged. Let me know if you find it to still be a problem.