Arthur Rand

Hello @nchernia, Sorry that the command isn't working. Regarding the program getting stuck. Could you run it with `--log ` and attach it here (or send it via email)? Maybe...

Hello @nchernia Would you be willing to share the BAM that causes the problem with me? I've been testing with 30-40x coverage on the whole genome and can't reproduce this...

@nchernia I may have found where the problem is. Could you try adding the following options to your command: ``` --super-batch-size 10 --batch-size 64 ``` If that works, you can...

Hello @nchernia, Ok good, glad it seems to have worked. > there are 8 more lines written in the version with --batch-size 64 Could you expand on this? Are they...

Hello @SuhasSrinivasan, There is a mention of the different versions in the [open chromatin documentation](https://nanoporetech.github.io/modkit/intro_open_chromatin.html#running-with-a-gpu) but I agree that it could be more useful. The README could also use a...

Hello @SuhasSrinivasan, > Since dorado has native support through PyTorch and Metal Performance Shaders, are there plans to provide a macOS binary for modkit? If there is sufficient users who...

Hello @SuhasSrinivasan, Yes, it's on my TODOs. For what it's worth, there isn't a v0.6.0 release of the `tch` and `candle` builds since the open chromatin module has not changed...

Hello @SuhasSrinivasan, Thanks for the suggestion. I'd be happy to accept a pull request if you like or I'll make the change in the next version.

Hello @baibhav-bioinfo, > (1) I have generated the bedmethyl file from bam file. Now i need a filter criteria for "coverage" and "mod_rate" to get rid of noisy predictions. You...

Hello @baibhav-bioinfo, > (1) what if we have more number of reads in one sample than other. Then the --min-valid-coverage cutoff might get biased towards the sample with more overall...