Supported Applications

gffread

Description

validates, filters, converts and performs various other operations on GFF files (use gffread -h to see the various usage options). Because the program shares the same GFF parser code with Cufflinks, Stringtie, and gffcompare, it could be used to verify that a GFF file from a certain annotation source is correctly "understood" by these programs. Thus the gffread utility can be used to simply read the transcripts from the file, and optionally print these transcripts back, in either GFF3 (default) or GTF2 format (with the -T option), while discarding any non-essential attributes, optionally fixing some potential issues with the input file(s).
Usage
To list all executables provided by gffread, run: $ biogrids-list gffread
Installation
Use the following command to install this title with the CLI client: $ biogrids-cli install gffread Available operating systems: Linux 64, OS X INTEL
Citation Note

Please cite the following url: https://ccb.jhu.edu/software/stringtie/gff.shtml#gffread

Keywords

Genomics, High-throughput sequencing, RNA-Seq Analysis
Default Versions

Linux 64: 0.11.6 (1.7 MB)
OS X INTEL: 0.11.6 (363.0 KB)
Other Versions
- OS X INTEL:
  0.9.12 (266.0 KB)
Developers

Geo Pertea