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ChristopherWilks / megadepth

BigWig and BAM utilities
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Scaling factor options? #15

Open biojiangke opened 2 years ago

biojiangke commented 2 years ago

Hi, megadepth has been a great tool! Thanks for the excellent utility! One question: is there an option to include a scaling factor when converting BAM to BigWig? Both UCSC utility and deeptools have that option implemented.

ChristopherWilks commented 2 years ago

Hi @biojiangke,

Thanks for the good words and the use of Megadepth!

There is no scaling factor option as you've probably determined already. However, I'll consider adding it in future.
In all honesty though, my focus is devoted to other projects now so I'm not sure when I'd do this.

Looking at the deepTools docs (https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html) it seems like the scaling factor option is only used for normalization. So to be clear are you asking for one or more normalization methods to be implemented in Megadepth (Megadepth does no normalization at this point) or something else that the scaling factor provides?

Thanks, Chris

biojiangke commented 2 years ago

Thanks for the quick response! Yes, we use the scaling factor primarily for normalization purposes, in particular on genome browsers to compare coverage across samples after normalization. So maybe it is not a crucial "must have" option but could be "icing on the cake" that would be good to have.

ChristopherWilks commented 1 year ago

@biojiangke thanks for the clarification. I can see the usefulness of normalization in the context you stated as well as potentially other uses. That said, implementing it is a non-trivial enhancement at this point, so as I said in the first response, I'm not sure when I'd get to this, but I'll keep it in mind.