An issue with gtf file (ballgownrsem)
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12 weeks ago

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

Ballgown RNA-seq GTF RSEM • 564 views
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I've run into problems in the past with malformed entries in ENSEMBL gtf files. Usually agat_convert_sp_gxf2gxf.pl from AGAT will resolve the issue.

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Thank you! After using this tool, I figured out that ballgownrsem can be run successfully only with GFF files.

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I also encountered issues when running ballgownrsem with gff files. Ballgown object was created, there is no informations about TPM and FPKM values for my samples. Does anyone have test files where ballgown objects are created properly ?

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