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streetslab / dimelo

python package for analysis of dimelo-seq & nanopore modified base data
MIT License
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Chromosome number in `methylationAggregate_` table #37

Open palakela opened 1 year ago

palakela commented 1 year ago

Hi, I was wondering, why does the aggregated table generated by the parse_bam function not report the chromosome number? I think keeping only the position can be misleading for the downstream analysis.

Is there maybe an easy way to include also this information in the table?

Thank you

thekugelmeister commented 1 year ago

Hi! Thank you, this is a great observation. We agree that this would be a good addition. We went back and discussed why the design is the way it is, and came to the conclusion that this simply did not affect any of the use cases we were targeting for the first release. However, the aggregate counts should be disambiguated by chromosome for other use cases and to improve clarity.

As an aside: we have come to the conclusion that this is NOT causing any bugs in the current versions of the analysis/plotting scripts. The methods that make use of the aggregate table do not currently have any need or even any way to disambiguate between chromosomes in downstream analyses. Any chromosome specification is done pre-parsing for these methods. We will update you if we find anything that refutes this claim.