To upload new genome references (or new versions), please follow these instructions:
1- Download the genome and annotation references from your species of interest from Ensembl (https://ftp.ensembl.org/ ).
Select the directory pub/
Select the release folder of your choice (e.g., release-110)
Select gtf/ folder or dna/ folder to download annotation or genome files, respectively.
Select your organism of interest
Download the gtf.gz file for the annotation reference
Download the toplevel.fa.gz file for the genome reference
2- Rename gtf and fasta files as follow:
Example: Mus_musculus.GRCm39.110.gtf.gz renamed to annotation_organism_ercc_sirv_biotyped.gtf
Example: Mus_musculus.GRCm39.dna.toplevel.fa.gz renamed to annotation_organism_ercc_sirv.fa
3- Create a gene_description .txt file.
The gene description.txt file is a tab separated file that contains two columns: Gene ID and Gene name.
To generate the gene_description file, please use the command line below. This command line uses the annotation file to extract the Gene ID and Gene name information.
((echo "Gene stable ID Gene name Gene description Chromosome/scaffold name Gene start (bp)") && (cat annotation_organism_ercc_sirv_biotyped.gtf | awk 'BEGIN{FS="\t"}{if($3 ~/gene/){if($9 ~ /gene\_id/ && $0 ~ /gene\_name/){match($9,/gene\_id \"([^\"]+)\"/); gid = substr($9,RSTART, RLENGTH); match($9,/gene\_name \"([^\"]+)\"/); gn = substr($9,RSTART, RLENGTH); map[gid] = gn }}}END{for(key in map){print key,map[key]}}' | sed 's/\"//g' | awk '{print $2"\t"$4"\t\t\t"}')) > gene_description.txt
4-Create a .bed file from the gft file.
To create a .bed file, please download the bedtools package and use the following command line:
gtf2bed < annotation_organism_ercc_sirv_biotyped.gtf > annotation_organism_ercc_sirv.bed
5- Generate a final directory containing both genome and annotation files.
Copy the files:
cp gene_description.txt annotation_organism_ercc_sirv.fa annotation_organism_ercc_sirv_biotyped.gtf annotation_organism_ercc_sirv.bed ./Directory_folder/
Compress the folder (tar.gz):
tar czfv Directory_folder.tar.gz Directory_folder
6- Upload the directory folder in Kangooroo as described in How do I upload my files in the Kangooroo platform?
7- Tag the reference as a genome file.
By default, all uploaded files appear as “File”. To be used as a reference by the pipeline, genome files must be marked as “Genome”. Please watch here our tutorial video to tag your file as Genome.
To change the file type, click on the file type icon in the type column to switch between file and genome. Once marked as “genome”, the file can be used as a reference in all your projects.