SycamoreLeaf

Based on the text in your screenshots, it appears Tombo is working correctly.

Hi @sr8510 . Welcome to GitHub! Would you mind copy-pasting the exact lines of code you run that lead to the error?

> [The produced per-base (and per-read) results are identical no matter the multi-processing options selected.](https://nanoporetech.github.io/tombo/modified_base_detection.html?highlight=multiprocessing#multi-processing) The per-read statistics file is really an HDF5 file. If you are not familiar with...

Hi @drivenbyentropy . I am not an ONT employee but I'll do my best to answer. I think the quantity you have described is the "fraction of modified reads" which...

> Based on your formula, _n_ corresponds to the total number of reads covering a particular position and not only those above the 0.5 threshold. Yep. > If this is...

Try removing the backslashes. Run `tombo resquiggle --help` for a summary of what each option does. All the options can be changed.

Hi @esand93. Welcome to Github! I'm not an expert at Tombo but I'll try to help with your first question. The error you referenced came from here in the source...

tl;dr Try specifying `--tombo-model-filename canonical-model` when you run `tombo build_model estimate_alt_reference`. Otherwise Tombo will use 6-mers. In the code that counts k-mers, the value of k is determined by `std_ref.kmer_width`:...

Your best bet is probably the [`tombo text_output`](https://nanoporetech.github.io/tombo/text_output.html) commands. If that doesn't have what you need, you can probably get it using the Tombo Python API. Instantiate a [`LevelStats`](https://github.com/nanoporetech/tombo/blob/afdb4d87249806d3a171d009f948f5b8558d35a0/tombo/tombo_stats.py#L3063) object...

Hi @aswathishiju . > Would it imply that the reference sequence which has Ts and the treated sample fast5s which has Us couldn't be aligned? Yes. Your treated sample is...