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dohlee / metheor

:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
GNU General Public License v3.0
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Documentation on output files #5

Closed GMFranceschini closed 1 year ago

GMFranceschini commented 1 year ago

Hi, thanks for developing metheor, the performance is impressive. Is it possible to have a detailed description of the meaning of column outputs? For example, in the case of PDR I get:

chr1    2036142 2036144 0.23076923  20  6
chr1    2036161 2036163 0.24444444  34  11
chr1    2036165 2036167 0.25531915  35  12

What are the last two columns? I think this information is not mentioned in the description or in the help. Thank you!

dohlee commented 1 year ago

Hi, thanks for trying out our tool. For now, the documentation has many things to be added including the output format, we'll make it updated soon! Feel free to report any other things that would be better to be described in the documentation :)

The last two columns represent the number of concordant sequencing reads (where all the meth. states of CpGs covered by the read are the same) and discordant sequencing reads (where more than one meth. states appear in the read) supporting that specific CpG. With that in mind, you can notice that the 4th column (PDR) is calculated as 6th / (5th + 6th). Hope this helps!

Best, Dohoon

GMFranceschini commented 1 year ago

Sure! I am very happy to provide feedback, the tools are wonderful, and I love that you used Rust. Also, more informative errors might help (badly formatted bed file, wrong paths...). I'll close the issue for now!

dohlee commented 1 year ago

Now the README file has the output specification with commit 4d8cb2f9fa0d4361539e168e087210c966fc378b. I'm commenting to this issue just for the reference. Thanks again!

Now I'm working on informative error handling, and hoping to have some updates soon.