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fiberseq / fibertools-rs

Tools for fiberseq data written in rust.
https://fiberseq.github.io/fibertools/fibertools.html
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Questions about ft extract and ft fire commands #54

Closed MariosEft97 closed 1 month ago

MariosEft97 commented 3 months ago

Hello! Thank you for developing such an amazing tool!

I have a few questions where I would greatly appreciate your insights:

  1. When using ft extract what does ‘-1’ represent for ns and as tags?
  2. Regarding ft fire command, if no model path is defined, are the FIRE calls based on the heuristics only, or is the available trained FIRE model used automatically?
  3. How 5mC calls (--use-5mc option) are used for FIRE calls?
mrvollger commented 3 months ago

Thanks for the questions, these ideally should all be documented, but I am always behind on that.

1) Positions in columns starting with ref_ maybe contain -1 (NA) values if the reference sequence has an insertion or deletion relative to the read sequence at that position.

2) A pre-trained FIRE model is used if none is specified. Training your own FIRE model is not recommended at this time. The pre-trained model is fairly robust to very different fiber-seq conditions.

3) 5mC calls are not used in FIRE currently. This was going to be a future option, but it should probably be removed because we have found it not very informative.

The docs and CLI will be updated in a future release.

mrvollger commented 1 month ago

These fixes have been applied in v0.5.0 we have started a documentation website to better answer these questions: https://fiberseq.github.io/