To upload new genome references (or new genome versions), please follow these instructions:
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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
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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
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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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gtf2bed <gtfToGenePred 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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6 - Upload the directory folder in Kangooroo as described in WORKING_COPYthe 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 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´´. Please watch our tutorial video on how to tag your file as a ´´Genome´´ type filehere.