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How to convert mod_mapping.bam to bed file #329

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JeremyQuo opened this issue Oct 31, 2022 · 3 comments
Open

How to convert mod_mapping.bam to bed file #329

JeremyQuo opened this issue Oct 31, 2022 · 3 comments

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@JeremyQuo
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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

@marcus1487
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--mod-binary-threshold . The default for this parameter is 0.8 as opposed to modbam2bed which has a default of 0.66.

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

@JeremyQuo
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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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