Genome browser - Jbrowser

Download Jbrowse

    wget http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=98
    cp Jbrowse-*.zip /var/www/
    cd /var/www/
    unzip Jbrowse-*.zip

Reference Visualize

    at /var/www/Jbrowse-*/
    ./bin/prepare-refseqs.pl --fasta mungbean_data/Total.fa --seqType 'dna' --out ./data/Vradi/

GFF Loading

    at /var/www/Jbrowse-*/
    ./bin/flatfile-to-json.pl -gff ./mungbean_data/mRNAerased.gff --out ./data/Vradi/ --trackLabel mRNAs --className transcript --getType --getPhase --getSubfeatures --getLabel --arrowheadClass transcript-arrowhead --subfeatureClasses '{ "CDS" : "match_part", "five_prime_UTR": "feature2", "three_prime_UTR": "feature2", "start_codon": "hourglass hgblue", "stop_codon": "hourglass hgred" }'

Adding Tracks

    echo '{ "maxFeatureScreenDensity": 1000, "label" : "wild Vradi SNPs", "key" : "wild Vradi SNPs", "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix", "urlTemplate" : "../../mungbean_data/wild2Total.fa.sorted.bam.bam.bvcg.bcf.d5D100.vcf.SNP.SCover100.gz", "tbiurlTemplate" : "../../mungbean_data/wild2Total.fa.sorted.bam.bam.bvcg.bcf.d5D100.vcf.SNP.SCover100.gz.tbi", "type" : "JBrowse/View/Track/HTMLVariants"} ' | ./bin/add-track-json.pl data/Vradi/trackList.json

Searchable by name or alias

    ./bin/generate-names.pl --out ./data/Vradi/ --verbose