readme

## Ref seq

cd to /export/prod/jbrowse_cassavabase/JBrowse-1.11.6/data/json
sudo mkdir cassavaV6_1
cd into it
Downloaded Mesculenta_305_v6.fa.gz from JGI <http://genome.jgi.doe.gov/pages/dynamicOrganismDownlo\
ad.jsf?organism=Mesculenta>
sudo bin/prepare-refseqs.pl --fasta Mesculenta_305_v6.fa.gz
sudo mv data/* .
sudo rm -r data

## Gene models

Downloaded all files within the v6.1 annotation folder at http://genome.jgi.doe.gov/pages/dynamicO\
rganismDownload.jsf?organism=Mesculenta
sudo unzip Mesculenta_download.zip
cd Mesculenta/v6.1/annotation
sudo gunzip Mesculenta_305_v6.1.gene.gff3.gz
sudo gunzip Mesculenta_305_v6.1.gene_exons.gff3.gz
sudo gunzip Mesculenta_305_v6.1.repeatmasked_assembly_v6.gff3.gz

#sudo ../../../bin/prepare-refseqs.pl --fasta /export/prod/jbrowse_cassavabase/JBrowse-1.11.6/data\
/json/cassavaV6_1/Mesculenta/v6.1/annotation/Mesculenta_305_v6.1.cds.fa.gz --trackLabel CDS --key \
CDS with# alternative splice variants --seqtype dna


sudo ../../../bin/flatfile-to-json.pl --gff /export/prod/jbrowse_cassavabase/JBrowse-1.11.6/data/j\
son/cassavaV6_1/Mesculenta/v6.1/annotation/Mesculenta_305_v6.1.gene.gff3 --trackType CanvasFeature\
s -trackLabel genes --clientConfig '{"description" : "note,description", "label" : "note,name,id" \
}' --metadata '{"category" : "mRNA"}' --out ./

sudo ../../../bin/flatfile-to-json.pl --gff /export/prod/jbrowse_cassavabase/JBrowse-1.11.6/data/j\
son/cassavaV6_1/Mesculenta/v6.1/annotation/Mesculenta_305_v6.1.gene_exons.gff3 --trackType CanvasF\
eatures -trackLabel genes with exons --clientConfig '{"description" : "note,description", "label" \
: "note,name,id" }' --metadata '{"category" : "mRNA"}' --out ./