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hasindu2008 / f5c

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)
https://hasindu2008.github.io/f5c/docs/overview
MIT License
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few sites from LSK114 #115

Closed ogrecio closed 1 year ago

ogrecio commented 2 years ago

Hi, I'm using f5c to call methylation sites from LSK114.

I'm obtaining only few sites. Is f5c ready to be used on LSK114? How should I implement f5c on reads from LSK114?

Thank you, Oscar

hasindu2008 commented 2 years ago

Unfortunately, we are still in the process of deriving a model for R10.4.1 (aka LSK 114). The current built-in models in f5c are for R9.4.1, so I am surprised it even picks a few sites in LSK114.

@hiruna72 is working on deriving a model - will let you know soon as we get it.

ogrecio commented 2 years ago

Thank you for the reply. Looking forward to it. Any tentative date? :-)

hasindu2008 commented 2 years ago

If it goes according to the plan, like one month. But these things rarely go according to the plan :D. So I would say a couple of months.

hasindu2008 commented 1 year ago

@ogrecio Sorry for the delay. Finally, we have a very crude methylation model for R10.4.1. Do you by chance have some data with a baseline suitable for testing?

ogrecio commented 1 year ago

Hi! we may have some data available. Maybe you can contact me privately and give me some details on what you would need.

Cheers, Oscar

hasindu2008 commented 1 year ago

On Twitter? Seems I cannot reach you there, possibly due to a setting. Could do on email if ou provide.

Also, if you are keen to try running, you can try the following steps:

git clone https://github.com/hasindu2008/f5c/ -b r10
autoreconf             
scripts/install-hts.sh  
./configure
make

Then, run the test script for r10:

scripts/test_lsk114.sh
head test/hg2_lsk114_reads_1000/meth.tsv # to see if there are any calls

Then, you should specify the options models manually using options --kmer-model test/r10-models/r10.4.1_400bps.nucleotide.9mer.template.model --meth-model test/r10-models/r10.4.1_400bps.cpg.9mer.template.model to f5c.

hasindu2008 commented 1 year ago

@ogrecio

I have done a prerelease f5c-v1.2-beta with the r10 models inbuilt. Tested on some human data and got ~0.9 correlation with bisulphite data (without filtering). Great if you can run on your samples and check if you get more methylation sites.