Difference between revisions of "AGAT"
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | [https://zenodo.org/record/3877441 Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format | + | [https://zenodo.org/record/3877441 Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format (Version v0.4.0). Zenodo.] |
| − | (Version v0.4.0). Zenodo.] | ||
|}} | |}} | ||
Latest revision as of 22:01, 15 July 2020
Description
It has the power to check, fix, pad missing information (features/attributes) of any kind of gtf and gff to create complete, sorted and standardised gff3 format.
The GTF/GFF formats are 9-column text formats used to describe and represent genomic features. The formats have quite evolved since 1997, and despite well-defined specifications existing nowadays they have a great flexibility allowing holding wide variety of information. This flexibility has a drawback aspect, there is an incredible amount of flavour of the formats, that can result in problems when using downstream programs.
Environment Modules
Run module spider AGAT to find out what environment modules are available for this application.
System Variables
- HPC_AGAT_DIR - installation directory
- HPC_AGAT_BIN - executable directory
Citation
If you publish research that uses AGAT you have to cite it as follows: