I'm running a re-annotation of some data with the ARA11 files, but I see there isn't a whole genome fasta file in the data download area. Are all of the .gtf and gff3 files relating to the TAIR10 genome, or is there another source which I should obtain it from?
The Araport11 release represents an update to the Genome Annotation *only*, the reference genome assembly version is still TAIR10.
The Araport11 release dataset represents an update to the Genome Annotation only (i.e. protein coding genes and non-coding RNA). This release is an incremental update to the TAIR10 gene set, by way of adding novel gene models, novel alternative splice variants, as well as correcting incorrect gene structures. The reference genome assembly (TAIR10) has not changed.
The TAIR10 genome assembly FASTA file is available for download at https://www.araport.org/downloads/TAIR10_genome_release/assembly
For more details about the methods used to generate the Araport11 annotation, see https://www.araport.org/data/araport11. To download the Araport11 Pre-release 1 data (July 2015), please see https://www.araport.org/downloads/Araport11_PreRelease_20150701.
Please note, an Araport11 Pre-release 2 dataset (October 2015) will be made available very shortly to the public via ThaleMine, JBrowse and bulk downloads. This release dataset is also being submitted to NCBI GenBank as an update to the existing TAIR10 records.
Vivek @ Araport