Arthur Rand

Hello @oneillkza, Understood. I'm actively working on some performance improvements and improving CRAM handling is on the work list. Would it be possible for you to share a few CRAM...

Hello @assafgrw, I often use Minimap2 (through Dorado `aligner`) in my experiments to map reads

Hello @jennyp76 Sorry for the delay getting back to you. tl;dr: The number of skipped reads increases for the reason you guessed, reads that don't overlap the regions in the...

Hello @CrisDAndres, sorry for the delay in getting back to you. > Can anyone explain what filters or criteria Modkit applies when generating the calls.tsv file? Why is the number...

Hello @eboileau, I think what you want is a command like this: ```bash modkit extract calls ${bam} stdout \ --filter-threshold 0.7 \ --ignore-index \ | awk -v OFS="\t" '(NR==1)||(($20=="false")&&($21=="false"))' ```...

Hello @eboileau, > the fail column would combine the effect of both --filter-threshold AND --mod-threshold, the result depending on whether we look at a modified base or not Correct. The...

Hello @kylepalos, Sorry for the delay, I was OOO last week. > Question 1: Is this a reasonable or correct approach to applying the motif arguments when analyzing all modifications?...

@kylepalos sorry for the delay - looking into this.

Hello @wangziyuan66, The 6mA_Inosine model is an all-context model, so all adenine residues will have a base modification call associated with them. All models have a false positive rate, so...

Hello @DexinYang1998, The model can be downloaded with one of the 0.5.0 [modkit releases](https://github.com/nanoporetech/modkit/releases/tag/v0.5.0). They all have the same model in the `models/` directory. Currently there is only one model,...