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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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Nanopore wgbstools vis #69

Open AzlanNI opened 7 months ago

AzlanNI commented 7 months ago

Hallo i am using wgbstools to visualize my Nanopore Data. So everything worked but i have a few questions regarding the Output. I segmented the Bam file and vis it with wgstools

wgbstools vis -r 1:14888-112659 -b Blocks_Barcode02_filt.bed.gz Barcode02_sorted.beta 1:14888-112659 - 97,772bp, 977CpGs: 190-1167 Barcode02_sorted : ..............................................0990.9999999999999.9..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................9

Thats how the region looks like for my first Segment on chr1. So my Question is now why are so many non values for these CpGs. I am bascalling with Guppy so i think there should be no problem with that. Cause if so many entries have no values does it not influence the avg methylation of my Segment ? And by that it would also influence my deconvolution with the uxm algorithm. Does anyone else have the same problem with nanopore and wgbstools ? Or maybe a solution for my problem ? Would be happy for any help!

Kind regards, Azlan

assafgrw commented 3 months ago

Did you use the --nanopore flag in your bam2pat command?