To upload new genome references (or new genome 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´´pub/´´
Select the release folder of your choice (e.g., release-110)
Select gtf´´gtf/´´ folder or dna´´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
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2 - Rename gtf and fasta files as follow:
gtf file : - annotation_organism_ercc_sirv_biotyped.gtfgtf
Example: Mus_musculus.GRCm39.110.gtf.gz renamed to annotation_organism_ercc_sirv_biotyped.gtf
fasta file : - annotation_organism_ercc_sirv.fafa
Example: Mus_musculus.GRCm39.dna.toplevel.fa.gz renamed to annotation_organism_ercc_sirv.fa
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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.
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4 - Create a .bedfile from the gft gtf file.
To create a .bed file, please download the bedtools package tools gtfToGenePred and genePredToBed and use the following command linelines:
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gtf2bedgtfToGenePred < annotation_organism_ercc_sirv_biotyped.gtf > annotation_organism_ercc_sirv.genepred genePredToBed annotation_organism_ercc_sirv.genepred annotation_organism_ercc_sirv.bed |
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5 - Generate a final directory containing both genome and annotation files.
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First, copy the files:
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cp gene_description.txt annotation_organism_ercc_sirv.fa annotation_organism_ercc_sirv_biotyped.gtf annotation_organism_ercc_sirv.bed ./Directory_folder/ |
Compress Then, compress the resulting folder (tar.gz):
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tar czfv Directory_folder.tar.gz Directory_folder |
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6 - Upload the directory folder in Kangooroo as described in the following FAQ: How do I upload my files in the Kangooroo platform?
7 - Tag the reference as a genome file.
By default, all uploaded files appear have a designated type marked as “File”. To be used as a reference by the pipeline, genome files must be marked as “Genome”the type of the uploaded file must be changed to ´´Genome´´. Please watch here our tutorial video on how 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 projectsa ´´Genome´´ type filehere.