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
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!
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