---
name: "pmrna"
section: "1"
platform: "linux"
package: "aegean"
version: "0.16.0+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pmrna"
---

# pmrna(1)

filter out all but the primary isoform from each gene of the input

## NAME

pmrna - filter out all but the primary isoform from each gene of the input

## SYNOPSIS

**pmrna** \[*options*\] *\< annot.gff3 \> new.gff3*

## DESCRIPTION

Options:

- **-h**\|--help

  print this help message and exit

- **-i**\|--introns

  flag indicating that introns are declared explicitly and do not need to be inferred from exon features; default is to infer introns

- **-l**\|--locus

  report a single representative mRNA for each locus instead of each gene

- **-m**\|--map: FILE

  write each gene/mRNA mapping to the specified file

- **-p**\|--pseudogenes

  disable pseudogene detection and correction