This repository contains pre-built images with CCTop stand-alone configured and ready to be used.
First we need to download the image
docker pull juanlmateo/cctop:latest
Then, we can use this image to run CCTop and the rest of the tools. In the next lines we have the commands to get CRISPR/Cas candidates for a sequence using the yeast as target species. This example shows all the steps, from creating the Bowtie index, the exon and gene files to the generation of the final output.
# downloading the genome of the target species in fasta format
wget ftp://ftp.ensembl.org/pub/release-99/fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz
# building the bowtie index from the fasta file
docker run -v `pwd`:/data/ cctop bowtie-build -r -f Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa.gz saccharomyces_cerevisiae
# downloading the annotation of this assembly in GFF format
wget ftp://ftp.ensembl.org/pub/release-99/gff3/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.99.gff3.gz
# generating the exon and gene files
docker run -v `pwd`:/data/ cctop gff2bedFiles Saccharomyces_cerevisiae.R64-1-1.99.gff3.gz saccharomyces_cerevisiae
# defining the input sequence(s)
echo -e ">YDL194W\nATGGATCCTAATAGTAACAGTTCTAGCGAAACATTACGCCAAGAGAAACAGGGTTTCCTA" > test.fa
# running CCTop
docker run -v `pwd`:/data/ cctop cctop --input test.fa --index saccharomyces_cerevisiae --exons saccharomyces_cerevisiae_exons.bed.gz --genes saccharomyces_cerevisiae_genes.bed.gz
Content type
Image
Digest
Size
494.7 MB
Last updated
about 6 years ago
docker pull juanlmateo/cctop