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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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Nanopore support #29

Closed oushujun closed 1 year ago

oushujun commented 1 year ago

Hello,

Thank you for developing fiber-seq and fiber-tools! I am new to this field. It seems that you can use the m6A-MTase treated gDNA to prepare Nanopore libraries and sequence with Nanopore, and there are many tools available to accurately call m6A in Nanopore data. My question: can Fibertools be used to process Nanopore-called m6A information by skipping the ft-predict-m6a step?

Thanks! Shujun

mrvollger commented 1 year ago

Hi @oushujun,

I think all the tooling should work fine with the Nanopore bams by skipping the predict step as you suggest. I know at least one person using ft add-nucleosomes with nanopore.

But let me know if you run into any issues, and I will be happy to address them if you can provide example data.

Cheers, Mitchell

oushujun commented 1 year ago

Thank you for the immediate response! Is this the right place to ask about the fiberseq m6A-MTase chemistry? I would like to obtain the currently most adaptative m6A-MTase and apply it in plants.

Thanks! Shujun

mrvollger commented 1 year ago

For that you should reach out to Andrew Stergachis (my PI) to see if you can get an MTA setup for the Hia5 enzyme. absterga@uw.edu

We are working on a protocol paper that covers both the wet and dry aspects of fiberseq but it's not ready yet...

Cheers, Mitchell

oushujun commented 1 year ago

Thank you Mitchell!

Shujun