I am currently trying out stuff and want to use my ONT Bam files as input for the uxm deconvolution algorithm. I was trying to generate the sliced pat files which only have entries which are present in the Atlas.U25.l4.hg19.tsv. According to the Tutorial i used
Please ensure that your file is TAB delimited (e.g., cat -t FILE).
Also ensure that your file has integer chromosome coordinates in the
expected columns (e.g., cols 2 and 3 for BED).
So i tried to adjust the tsv file to have the 5 columns 'chr' 'start' 'end' 'startCpG' and 'endCpG' in the bedfile only and ensured that the file is tab-delimited.
wgbstools view -L Atlas.U25.l4.hg19.bed Left_Ventricle_STL001.IGF2.pat.gz
So i still got the same Error. And now i was trying too look for the basecode to understand why this Error is occurring but i did not find the Error Message in the view.py or cview.cpp files. Maybe someone could help me out.
The Left_Ventricle file i got from wgbs_tools/tutorials and the Atlas i got from /UXM_deconv/supplemental. I was just trying how how to filter the pat file to only have the entries which are included in the Atlas for my later usage. In the Zip file i just uploaded my files if anyone wants to have a look at them.
I removed the headers from the .bed file and it created a Intersected document which is empty. Is it cause there are no overlaps between these both files i am using ?
AzlanNI
commented
2 months ago
Test1.zip Hello everyone!
I am currently trying out stuff and want to use my ONT Bam files as input for the uxm deconvolution algorithm. I was trying to generate the sliced pat files which only have entries which are present in the Atlas.U25.l4.hg19.tsv. According to the Tutorial i used
wgbstools view -L Atlas.U25.l4.hg19.tsv Left_Ventricle_STL001.IGF2.pat.gz
I got
So i tried to adjust the tsv file to have the 5 columns 'chr' 'start' 'end' 'startCpG' and 'endCpG' in the bedfile only and ensured that the file is tab-delimited.
wgbstools view -L Atlas.U25.l4.hg19.bed Left_Ventricle_STL001.IGF2.pat.gz So i still got the same Error. And now i was trying too look for the basecode to understand why this Error is occurring but i did not find the Error Message in the view.py or cview.cpp files. Maybe someone could help me out.
The Left_Ventricle file i got from wgbs_tools/tutorials and the Atlas i got from /UXM_deconv/supplemental. I was just trying how how to filter the pat file to only have the entries which are included in the Atlas for my later usage. In the Zip file i just uploaded my files if anyone wants to have a look at them.
I removed the headers from the .bed file and it created a Intersected document which is empty. Is it cause there are no overlaps between these both files i am using ?
I am thankful for any advice! kind regards, Azlan