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shishenyxx / DeepMosaic

DeepMosaic is a deep-learning-based mosaic single nucleotide classification tool without the need of matched control information.
https://www.nature.com/articles/s41587-022-01559-w
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running DeepMosaic with hg38 #4

Closed tgambin closed 1 year ago

tgambin commented 1 year ago

Hi, I am trying to run DeepMosaic with hg38 and I found one resource is missing:

'Error: The requested file (/resources/all_repeats.hg38.bed) could not be opened. Error message: (No such file or directory). Exiting!'

Do you have this file ? Or could you provide description how to generate it? Thanks!

shishenyxx commented 1 year ago

Hi, I am trying to run DeepMosaic with hg38 and I found one resource is missing:

'Error: The requested file (/resources/all_repeats.hg38.bed) could not be opened. Error message: (No such file or directory). Exiting!'

Do you have this file ? Or could you provide description how to generate it? Thanks!

Hi, we have added all_repeats.b38.bed and segdup.hg38.bed to the resource folder.

They were just generated from UCSC genome browser, sorted and merged with bedtools.

Best,

Xiaoxu

tgambin commented 1 year ago

Thanks! Now it works and I was able to get predictions to my mosaic variants :).

shishenyxx commented 1 year ago

Thanks! Now it works and I was able to get predictions to my mosaic variants :).

Glad to hear that. Thank you for your interest in DeepMosaic!