To upload new genome references (or new genome versions), please follow these instructions:
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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 How do I upload my files in the following FAQ: How do I upload my files in the Kangooroo platform?
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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.