Radmeth regression for MLML data

[Chris S]

Hi, 

From what I see, the output of MLML data is not formatted in a way to be useful for Radmeth given that the data is split across 3 columns: hmC, mC, and C. Would it be possible and appropriate to create pseudo read counts and coverage of hmC for multiple files, combine those data files with methcounts merge, and then utilize radmeth regression? 

I expect this would be possible, however, doing so would need some guidance on the levels of pseudo hmC. If it were 20% hmC, would that be best represented as 8 coverage, 2 hydroxymethylated reads, or 80 coverage and 20 hmC reads? This example is simple, but more diverse estimations like 24% or 35% would be poorly served by approximating them with values less than 10. 

Thank you for all the help,

Chris

[Andrew D. Smith]

Can you state the hypothesis you would be testing with the radmeth regression at each site?

Andrew

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[Jianghan Qu]

Hi Chris,

Could you checkout the latest version of methpipe on github?
MLML is now part of Methpipe. Further development will be done within
Methpipe as well.

This issue had come up repeatedly. We made an update to MLML per user
request to generate pseudo methcount files that are compatible with
other Methpipe tools.
With options -H or -M, MLML now can output methcount format files with
pseudo read counts for 5hmC or 5mC.

Please let us know if you have any questions. Thanks!

Best,
Jianghan

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