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Feature request

Open kamaloxfordpathology opened this issue 1 year ago • 2 comments

Hi, Awesome tool!. Could we have a feature similar to deeptols computeMatrix for creating metagene profiles of modification pattern. Thanks.

Regards, Kamal

kamaloxfordpathology avatar Jan 09 '25 07:01 kamaloxfordpathology

Hello @kamaloxfordpathology,

The modkit localize command is intended for this task, however it is probably not quite as fully-featured as the command in deeptools. Depending on what you're trying to do, maybe you can use the output table from modkit to get the visualization you are looking for?

I'd like to add some more features to this command in the future, if there is a specific feature in deeptools that you want I can prioritize it.

ArtRand avatar Jan 09 '25 14:01 ArtRand

Hi @ArtRand ,

Thanks for the reply. Yes, modkit localize could used for reference point based pattern calculation similar to deepTools computeMatrix refernce point. However, a feature similar to computeMatrix scale region would be appreciated. Currently, I am proceeding by converting my modkit pileup output to a bedGraph (with percentage modified as score in column 4) and then to a bigWig file, From there, I can employ deepTools computeMatrix on these bigWig files. Thanks

Regards, Kamal

kamaloxfordpathology avatar Jan 09 '25 15:01 kamaloxfordpathology