Chris Faulk

I have the same question. I have recently used megalodon to basecall mammalian mitochondrial reads from a 9.4.1 minion run. Most were at 0%, as expected, but overall, the average...

Thanks for the detailed response. I used megalodon rather than guppy because I already had an assembled genome that I wanted to get methylation calls for, rather than calling with...

Just an update. I re-ran the basecaller with guppy, using the old research model with >80% stringency, `res_dna_r941_min_modbases_5mC_5hmC_v001` and got: 0.2% 5hmC 0.13% 5mC Then I ran the updated model,...

Hi @kaanokay , Yes I have dealt with that issue in the following way. Concatenate all the unmapped bam files containing modified base information. `samtools cat -o mod_basecalls.bam *input.bam` Map...

I have the same question. Anyone have a suggestion?

@surabhiranavat Thanks for the idea. I used seqkit instead and I'll cross-post what I did from the same question on ONT's community site. 1) Run guppy to call simplex 2)...

Megalodon input works great for me, using the mod_mappings.bam. However I don't like the color. It's just a light beige to dark red palette. Is there a way to specify...

I'm a little confused on how to show different modifications. In my case, I am using a mod_mappings.bam that I sorted and loaded into methplotlib. It has calls for both...

Thanks Marcus, I see the issue. I called bases using the rerio 5mC+5hmC model and honestly I found it to work very well. The genome is mitochondria and I saw...

Oh yes sorry, I should have gotten back to you to close this. Following your last comment, "`--filter-threshold A:1.0` sets the canonical A threshold to an unachievable 1.0, so all...