# working folder
/var/www/jbrowse/Elrike_2015_08

# format refseq 
bin/prepare-refseqs.pl --fasta docs/bcereus/combined.fna

# add annotation
bin/flatfile-to-json.pl --gff docs/bcereus/combined.gff --trackLabel Original_Annotation --trackType CanvasFeatures
# make feature searchable
bin/prepare-refseqs.pl -gff docs/bcereus/combined.gff
bin/generate-names.pl

# make link to the data/ folder
ln -s /home/anne/PROJECTS/Elrike/2015_08_joaquin Elrike_2015_08_joaquin

# make config file
# data/tracks.conf
# add tracks to this file

# If BAM is empty, check the genome header name
/usr/molgentools/tools/find_and_replace_single.pl -i MG1363_A.sorted.bam -f 'gi|125622882|ref|NC_009004.1|' -r 'NC_009004.1' -o MG1363_A.sorted.new.bam