mollybrothers

Megalodon can take a list of readIDs to analyze, right? So is a possible (somewhat silly) workaround for this to run guppy basecaller and then barcoder separately from megalodon, extract...

I appreciate the complexity, so thank you for the additional possible workarounds!

Sounds reasonable to me for those that want aggregated reads separated by barcode. I'm also very interested in getting the `per_read_modified_base_calls.db` and/or `per_read_modified_base_calls.txt` separated by barcode as well. The SAM/BAM/CRAM...

If you have a list of read IDs (as a .txt file) that correspond to a given barcode, you can feed it into megalodon using `--read-ids-filename $READ_IDS` flag and megalodon...

I'm not totally sure whether megalodon works for single fast5 files (which looks like the output from the demultiplexer you linked above). I would look at the megalodon documentation. I...

@amauryavril it does look like single fast5 files are supported (https://nanoporetech.github.io/megalodon/common_arguments.html?highlight=single%20fast5#required-argument)

Hi Marcus, I can provide some context (Koen and I are working together). 1. We used the all-context rerio model `res_dna_r941_min_modbases-all-context_v001.cfg`. Looking at that model's distribution of mod probs (thanks...

Thanks for the great explanation, Marcus. We _are_ looking for m6A DNA methylation, so we'll keep an eye out for any updates to the rerio models. I want to make...