An issue with gtf file (ballgownrsem)

[darko-cucin]

Hi everyone,

When I tried to run ballgownrsem I encountered an issue which was caused by the inappropriately structured GTF file. Also, I tried to run code which is part of ballgownrsem and did not find the root of the issue. GTF files are mainly GTF files which are available at the public repositories (Ensembl…). As file is larger I can not attach the file but I will attach the link to directory: Homo_sapiens_GRCh38.110
The error message is as follows:

Mon Dec 4 09:33:09 2023
Mon Dec 4 09:33:09 2023: reading annotation
Mon Dec 4 09:35:50 2023: handling exons
Mon Dec 4 09:36:05 2023: handling introns
Error in .width_as_unnamed_integer(width, msg = "an end that is greater or equal to its start minus one") :
each range must have an end that is greater or equal to its start minus one

I understand that the start position of the intron is higher than the end position. But I do not understand how it happened.

Kind regards,
Darko Cucin