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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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genome "liftover" for pat format #46

Closed NikolausMandlburger closed 1 month ago

NikolausMandlburger commented 1 year ago

Hi! Thank you for developing these great tools! I was wondering what would be the recommended way to convert pat files from one genome to another? As far as I am aware there is no designated function for this in wgbstools. I would be interested in this kind of functionality because I would like to transfer the cfDNA pat files from your 2023 nature paper from hg19 to hg38. Thank you in advance, all the best, Nikolaus

AndriesDeKoker commented 1 year ago

From the references folder of the wgbs_tools, I have merged the coordinates in the hg19 CpG.bed.gz, based on clusterID, with the hg19 pat-file. I used LiftOver on the coordinates to go from hg19 to hg38 coordinates. Merged based on the coordinates the hg38 CpG.bed.gz clusterIDs and selected the columns necessary for a pat-file, bgzipped to get the hg38 pat.gz

NikolausMandlburger commented 1 year ago

Thank you very much!! Am I right that I have to subtract 1 from the start column of the CpG.bed.gz file (1 based) to work correctly with lift over which expects 0 based bed files?

AndriesDeKoker commented 1 year ago

Yes, indeed, I also did that!

NikolausMandlburger commented 1 year ago

great, thanks a lot!!