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/). To achieve this you should:
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:
gtf file - annotation_organism_ercc_sirv_biotyped.gtf
Example: Mus_musculus.GRCm39.110.gtf.gz renamed to annotation_organism_ercc_sirv_biotyped.gtf
fasta file - annotation_organism_ercc_sirv.fa
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.txt file, please use the command line presented 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. To do this you need to:
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 resulting folder (tar.gz):
tar czfv Directory_folder.tar.gz Directory_folder
6 - Upload the directory folder in Kangooroo as described in WORKING_COPY: 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 have a designated type marked as “File”. To be used as a reference by the pipeline, the type of the uploaded file must be changed to ´´Genome´´ genome files must be marked as “Genome”. Please watch here our tutorial video on how to tag your file as a ´´Genome´´ type file here.
To change the file type, click on the file type icon (Can we insert the icon here?) in the type column to switch between ´´Ffile´´ and ´´Ggenome´´. Once marked as “Ggenome”, the file can be used as a reference in all your projects.