Arthur Rand

Hello @SuhasSrinivasan > Just to confirm modkit sample-probs --no-filtering is the go to method to scan for modification probabilities? Correct. Although it can consume a lot of memory right now...

@SuhasSrinivasan, If you have a BAM that is extracted from a region, or has

Hello @SuhasSrinivasan, I apologize, I had the flag incorrect, the correct flag for `sample-probs` is `--no-sampling`. I've made some adjustments based on your other issues so that the command line...

Hello @SuhasSrinivasan, These are hard-coded warnings meant to signal something may be off. I can see that it's redundant when you've set the values manually, but I think it's still...

Hello @SuhasSrinivasan, No problem. The sampling still happens and you'll see these log lines: ```text > Using filter threshold 0.9042969 for C. > Using filter threshold 0.9511719 for T. >...

Hello @Ge0rges, I agree that the BED file should direct the strand to use. I'll be sure to add it along with the multi-base work.

The final log will report `0 regions processed successfully` in this case. There is always a bit of a balance to strike with respect to informing the user why something...

Hello @Ge0rges, The schema is: | col | Name | Description | type | |-----|------|-------------|------| | 1 | chrom | chromosome of the region | str | | 2 |...

Hello @kamaloxfordpathology Sorry for the terribly long response time (new Modkit features are coming!). Do you mean calculate a metric for m6A vs ¬m6A (so Inosine and unmodified will be...

Hello @kamaloxfordpathology > shall I I split the modkit pileup data using adjust mods separately for m6A and Inosine and then perform differential modification analysis for each of them? Actually,...