Maxime U Garcia
@maxulysse.github.io
Bioinfomagician/PhD in Bioinformatics, developing @nextflow.io @nf-co.re pipelines
Posts and RPs in English/French - He/him
Posts and RPs in English/French - He/him
January 16, 2026 at 4:01 PM
- Remove all GTF entries without proper strand (this is especially appropriate if those entries are not meant to denote proper exons or transcripts anyway, but something else).
January 16, 2026 at 4:01 PM
- Remove all GTF entries without proper strand (this is especially appropriate if those entries are not meant to denote proper exons or transcripts anyway, but something else).
- Find a better GTF. (Have a look at Ensembl; I have a GTF from release 108 lying around which only has + or - in the strand column.)
- Find out what the strand should be and replace the ? with the appropriate symbol.
- Find out what the strand should be and replace the ? with the appropriate symbol.
January 16, 2026 at 4:01 PM
- Find a better GTF. (Have a look at Ensembl; I have a GTF from release 108 lying around which only has + or - in the strand column.)
- Find out what the strand should be and replace the ? with the appropriate symbol.
- Find out what the strand should be and replace the ? with the appropriate symbol.
From a community member on Slack:
Transcripts are inherently stranded, so ? as strand does not make sense, and any tool has no choice but to refuse to deal with this.
Work-arounds (in order of preference):
Transcripts are inherently stranded, so ? as strand does not make sense, and any tool has no choice but to refuse to deal with this.
Work-arounds (in order of preference):
January 16, 2026 at 4:01 PM
From a community member on Slack:
Transcripts are inherently stranded, so ? as strand does not make sense, and any tool has no choice but to refuse to deal with this.
Work-arounds (in order of preference):
Transcripts are inherently stranded, so ? as strand does not make sense, and any tool has no choice but to refuse to deal with this.
Work-arounds (in order of preference):