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weir12 / DeepEdit

DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using Nanopore direct RNA sequencing
MIT License
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Can deepEdit detect the most confidence site in the region? #15

Closed JeremyQuo closed 1 year ago

JeremyQuo commented 1 year ago

There is a special bed file that required by DeepEdit. I want to know if I can input a bed annotated some region. And deepedit told me the most confidence sites. Many thanks if can help

JeremyQuo commented 1 year ago

If not, we need to extract all A bases on our reference and build a site level bed to see all the prediction on it?

weir12 commented 1 year ago

Dear JeremyQuo,

Thank you for your interest in DeepEdit and for reaching out to our team. We appreciate your attention to our work. However, we regret to inform you that the current version of DeepEdit does not support the direct input of a BED file annotated with specific regions or provide predictions for those regions.

Thank you for your understanding, and we wish you success in your research.

Best regards, Ou Liang

JeremyQuo commented 1 year ago

Thanks for your reply