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gxelab / psite

Model-based inference of P-site offsets for ribosome footprints
MIT License
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Question about using PSite output for downstream analyses #2

Closed andresferben closed 4 months ago

andresferben commented 4 months ago

Hi there,

I wanted to ask if you analyzed the feasibility of combining PSite's output with Ribotricer for ORF prediction as you did with Ribo-TISH and RiboCode. Do you think this would be possible?

Thanks

mt1022 commented 4 months ago

Hello, We have not yet attempted this approach. Nonetheless, it is technically feasible. The ribotricer tool infers the P-site offset for each read length and merges reads based on the estimated offsets within the detect_orfs.py script. It is plausible that the P-site offset tags per read, as determined by the PSite algorithm, could be utilized at this stage to supersede the offsets estimated by ribotricer. For more details, you can refer to the relevant section of the detect_orfs.py script in the ribotricer repository: detect_orfs.py.

andresferben commented 4 months ago

Thanks! I'll take a look at it.