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How to convert mod_mapping.bam to bed file #329

Open

JeremyQuo opened this issue Oct 31, 2022 · 3 comments

JeremyQuo commented Oct 31, 2022

I used modbam2bed package(default setting 0.33 0.66)
But the result is different with modified_basexxx.bed.
Is there any command or code that can generate the same file

Collaborator

marcus1487 commented Oct 31, 2022

--mod-binary-threshold . The default for this parameter is 0.8 as opposed to modbam2bed which has a default of 0.66.

marcus1487 mentioned this issue

How megalodon get the threshold when load remora model nanoporetech/remora#40

Closed

PanZiwei commented Oct 31, 2022

I thought the parameter is 0.75 now instead of 0.8 based on the modified base arguments?

Author

JeremyQuo commented Oct 31, 2022

Thanks! I thought that there will be a mechanism that will decide the thresholding dynamically when we trained our own model in remora.Anyway.Thank you

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