Arthur Rand

Hello @ZhihanNUS, The `pileup` command will only use primary alignments to generate the bedMethyl table. If there are errors with records in the modBAM file you can inspect the reasons...

Hello @ZhihanNUS, > Since there is no skipped reads, does it mean modkit pocessed all reads in bamfile, or there is any other rules to filter some reads? Can you...

Hello @hoppo The `pileup` function doesn't count every read that is skipped. The skipped count are primary alignments that are not used in the aggregation, you could call this "fail...

Hello @ZhihanNUS, The log you sent doesn't have any messages with reads that have errored. The estimated pass threshold for A-modifications (0.6347656) is lower than I might expect. Could you...

Hello @Adinivich, > Since the thresholds change methylation status so much, what do you recommend as --filter-threshold and --mod-thresholds (if that even plays a role in combination with --filter-threshold)? Is...

Hello @Adinivich, Thanks for sending those data over. The distributions of output probabilities in your data is indeed a little difficult to interpret. The latest version of modkit ([v0.3.2](https://github.com/nanoporetech/modkit/releases/tag/v0.3.2)) has...

@Adinivich feel free to re-open this issue if you have additional questions or have difficulty running the new `sample-probs` command.

@Ge0rges, I agree, the parsing errors should be more informative. I'll fix that. Could you tell me which version of `modkit` you used to generate the input data (the pileups)?...

@Ge0rges I'm going to re-open this issue to track work for better error messages when input fails to parse. Some other users have encountered the same error and it's not...

Hello @Rpowellnz, Could you tell what ```bash $ head -n 5 refseq.bed ``` looks like?