Marcus Stoiber

Setting to 4 is equivalent to `-4 4` which is probably a good threshold here. Here the first value indicates that any log likelihood ratio lower is considered modified while...

Was setting this value able to resolve this issue sufficiently?

I can confirm @Chris-Kimmel 's answer. Tombo models require that all values of the k-mer must be observed in order to produce a model. There are no workarounds for this...

This is a great summation of the issue by @Chris-Kimmel . Not sure I have much to add. Let me know if you have any further issues with these commands.

The `tombo build_model estimate_motif_alt_reference` command does not take the `--tombo-model-filename` argument. Instead this command takes the `--upstream-bases` and `--downstream-bases` arguments as in the canonical model training command. It is left...

This error is occurring since one of the k-mers contained within the `--motif-description` is not covered by the sample provided at the depth defined by `--minimum-test-reads`. You can try to...

Ah. The bed file is your issue. What is the use case that you are aiming for? I would certainly not recommend training a model from a single location. The...

Thank you for this bug report and extra effort to debug! I'll have to take a closer look, but it seems that this might actually be an issue with the...

Yes, I believe this is simply a cosmetic issue, but have not had a chance to investigate the root of this issue yet.

There are a number of possibilities here. What was the output of the resquiggle commands for these runs? The main other thing to check would be that these two samples...