If you would like us to add a new genome to CHOPCHOP, please submit a genome assembly file (FASTA) and gene annotation file (GFF3) corresponding to your organism of interest. In addition, to avoid errors when uploading these files to CHOPCHOP, please complete the following tasks before submission:
- Ensure your gene annotation file is a valid GFF3 file. To validate your file, please run gff3ToGenePred and ensure there are no errors. You will need to run this program on the terminal. If you are unsure how to do that, please ask someone (e.g. a bioinformatician) to help you.
- Check that the ID attribute in the GFF3 file corresponds to the identifier you want to use for looking up genes. For instance, in this line (ID=gene6;Name=NCU09906;gbkey=Gene;gene_biotype=protein_coding;locus_tag=NCU09906) of a GFF3 file, the gene name that will be searchable in CHOPCHOP is “gene6”. If you would prefer it to be the value in the Name attribute (“NCU09906”), please let us know.
- Ensure that the chromosome names are identical across the GFF3 and FASTA files, and the gene coordinates correspond to the genome FASTA file.
When all of this is fulfilled, please send us a request by email.