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zolotarovgl / GeneExt

GeneExt - Gene extension for improved scRNA-seq data counting
GNU General Public License v3.0
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0-coordinate bug #7

Closed zolotarovgl closed 3 months ago

zolotarovgl commented 3 months ago

Sometimes, the features tend to get start coordinate = 0

SamiLhll commented 3 months ago

Hi ! Great tool ! I had this issue which is a problem when using cellranger afterward. I'm writing this comment so I can have a notification when you solve the problem. Good luck !

zolotarovgl commented 3 months ago

Dear Sami,

It’s a minor bug - I will solve it in the next commit. For now, you can just fix it using awk:

awk ‘{if($4==0}{$4=1};print $0}’ GTF > GTF.fixed

zolotarovgl commented 3 months ago

It's fixed now.

SamiLhll commented 3 months ago

Awesome ! Thank you very much !

zolotarovgl commented 3 months ago

Thank you for commenting on the issue! Please, let me know if you encounter any other bugs.