Issue with bed file for read_distribution.py

[Asmita Shrestha]

Hi, I need bed file of sus scrofa  appropriate for read_distribution.py. I tried making with gtf file https://ftp.ensembl.org/pub/release-112/gtf/sus_scrofa/Sus_scrofa.Sscrofa11.1.112.gtf.gz. I could successfully make 6 column bed file, but I am unable to make 12 column bed file. I tried to convert my 6 column bed file to 12 column format following her: 

Dec 8, 2020, 4:53:04 AM

to rseqc-discuss

Hi,

I think I figured it out after sending the previous email.

Actually the original 6 column bed file from USCS table browser will work after adding column 7 to 12:

column 7 = column 2

column 8 = column 3

column 9 = 0

column 10 = 1

column 11 = column 3 - column 2

column 12 = 0

But running this kind of bed file in read_distribution.py didnot give any output on UTR exons. So i am in need of proper 12 format bed file suitable for read_distribution.py