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jts / mbtools

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Mean modification frequency: NaN #4

Open Rodcarlessi opened 1 year ago

Rodcarlessi commented 1 year ago

Hi guys,

I am trying to use mbtools but am getting zero total_calls and modified_calls for all reads. My data is modbams called with dorado using model dna_r10.4.1_e8.2_400bps_sup@v4.1.0 and --modified-bases 5mCG_5hmCG.

Any idea how to address this problem? Has anybody experienced this issue?

Many thanks! Rodrigo

Rodcarlessi commented 1 year ago

Hi again,

Just to report that I figured what seems to have been causing the problem in case anyone encounters the same issue.

Apparently, the 5hmCG calls were the problem. I used modkit adjust as follows to remove 5hmCG calls from the bam prior to passing to mbtools and this solved the issue.

modkit adjust-mods input.bam output.adjust.bam --ignore h

jts commented 1 year ago

Hi @Rodcarlessi,

Thanks for following up! That's good to know. When I have a bit of time to come back to mbtools I'll try to make sure I handle this case.

Jared

hrrsjeong commented 1 year ago

I had the same issue. Thanks @Rodcarlessi