Nanopore Data about uxm_deconv HOT 2 OPEN

So i know tried out a lot and got to a Problem. I am using Guppy for basecalling and generating .bam files. After that i used wgbstool to generate .pat and .beta files from the .bam file. Now i am trying to use the .pat File i got from wgbstools to deconvolve with uxm. So my command ist
uxm deconv Barcode02_sorted.pat.gz -o Output.csv
And it is giving me:
Invalid input argument
Length of values (2) does not match length of index (36)

I tried the following:
I got the markers from
tail -n +2 Atlas.U250.l4.hg19.full.tsv | cut -f1-5 > markers_Atlas.U250.l4.hg19.full.bed
And used wgbstool view -L to filter my pat file
wgbstools view -L /Users/azlannisar/UXM_deconv/supplemental/markers_Atlas.U250.l4.hg19.full.bed Barcode02_sorted.pat.gz --min_len 4 --strip --strict > Barcode02_Nano_sorted.stripped.pat

After that my File is empty so i guess i dont have any Regions which are overlapping ? So how should i go on can i somehow adjust the marker file or is it not possible for Nanopore Data.

I am thankful for any help!
kind regards,
Azlan

from uxm_deconv.

after using
wgbstools homog -b blocks_Barcode02.bed.gz -f Barcode02_sorted.pat.gz
i get WARNING: all zeros!
But i generated the files from the same .bam file
I looked more into it and generated the blocks file with this command:
wgbstools segment --genome GENOME_NAME -F Barcode02_sorted_ascii.beta -o blocks_barcode02_new.bed
The GENOME_NAME file is the same reference i generated the bam file with. And if i look into the first entries of the pat, beta and blocks file it looks like this
Pat :
(base) azlannisar@Air-von-Azlan Desktop % head -n 10 Barcode02_sorted.pat
1 236 TCCT.CCCCCCCCCCCCC.C 4
1 1166 CTTTC.T 4
1 1187 TTTTCCCCCCC 4
1 1194 CCCCT.CCCCCTCCCCCCCCCCCCCCCC 4
1 2046 TTCCCCTCT 4
1 2048 C.CCCC....CCC..C.T.TCCCCTCCCC...C.CC..CTCC 4
1 2133 CTT.C.TCCCCT.CCC.CCC 4
1 2153 C..C.TCC..CCCCCTT.CCCCCCC..C.CT.CCCC.T.CTC 4
1 2192 C 4
1 4067 TCCCC.CCCCCCCCCCCCCCCCTT..TTTTTTCCCCCCCCCCCCCCCCC.CCCCCCCT.TTCTCC.CCCCCCCCCCCTCC.C.C.T.CCCCTCCCCCCC 4
beta:
(base) azlannisar@Air-von-Azlan Desktop % head -n 10 Barcode02_sorted_beta.bed
1 16821 16823 0 4
1 16868 16870 4 4
1 16931 16933 4 4
1 16943 16945 0 4
1 16973 16975 4 4
1 17377 17379 4 4
1 17405 17407 4 4
1 17451 17453 4 4
1 17477 17479 4 4
1 17482 17484 4 4
Blocks:
head -n 10 blocks_barcode02_new.bed
1 10469 10782 1 55
1 10783 12783 55 154
1 12807 14792 154 190
1 14888 16823 190 237
1 16962 17716 240 256
1 17853 19789 256 304
1 19888 21818 304 348
1 21948 23844 348 375
1 23974 25934 375 403
1 25974 27970 403 430
So i guess my mistake is in the segmentation if i am not mistaken. Do i have to toggle something like in bam2pat with. -np for nanopore Data ?

from uxm_deconv.