Radmeth Output

[Chris S]

Hi, 

It was previously discussed that the outputs for methdiff and radmeth would report the number of unmethylated reads in A, methylated reads in A, unmethylated reads in B, and methylated reads in B for the last 4 columns of the output. 

With the release of methpipe-master, it seems to me that these may not be appropriate definitions for the columns. Are the columns actually coverage, and number of methylated reads as described in the manual? How are these columns calculated, from the average across the sample groups, or from the sum total across the groups?

Thanks,

Chris

[Meng Zhou]

Hi Chris,

Thanks for pointing this out. The format does differ for these two programs. Methdiff uses unmeth read and meth read, while radmeth uses coverage and meth read. For now we will fix the description in the manual to make sure it reflect the correct format. In the future we will change the format of either program to make it consistent and less confusing.

Best regards,
Meng

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[Chris S]

Hi Meng, 

Thanks for the clarification. 

Are these differences in the input accounted for in the software? I typically use MethPipe, followed by the merge-methcounts function. Does merge-methcounts convert the unmethylated/methylated reads into a coverage/methylated reads output suitable for Radmeth?

Best,

Chris

[Meng Zhou]

The changes have not been made for programs yet. Currently only the manual is updated. For merge-methcounts, the -t option for tabular format output is meant for radmeth, which has methylated reads and total coverage for each sample.

Best regards,
Meng

[Chris S]

Thanks again Meng!

I appreciate how responsive and helpful everyone has been! I have been using -t for merge-methcounts, to continue into radmeth, glad this is how it works.

Best,

Chris