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I get 'Annotation name 'ADV5_annot' not found in this database' in step talon_abundance #118

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thadasps opened this issue Jan 2, 2023 · 1 comment

thadasps commented Jan 2, 2023

Hi, I follow the way to solving this problem in https://github.com/mortazavilab/TALON.wiki.git and when I use

awk '($3 != "gene")' adv5_gtf.gtf and talon_reformat_gtf -gtf adv5_gtf.gtf.

I got this error

Can you point me to solve this?

If you want to reformat gtf file. I upload data in this link : https://drive.google.com/drive/folders/1SUfKoZiFfX9AjXWs2mrEKh9dvf87xDwA?usp=sharing

yxsee commented Jan 3, 2023

Try
awk '($3 != "gene")' adv5_gtf.gtf > adv5_gtf_no_genes.gtf
talon_reformat_gtf -gtf adv5_gtf_no_genes.gtf

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