# working folder
	/var/www/jbrowse/Jay_Zhu

	
# empty the folder docs/fna
# empty the folder docs/gff
# empty the folder data/names
# empty the folder data/seq
	
# Copy Genome Info to the fna and gff folders
	copy all fna to ../docs/fna
	copy all gff to ../docs/gff

	cp /var/ngs/bowtie_indexes/bowtie_indexes/NC_000964.fna /var/www/jbrowse/Mirjam_Boonstra/docs/fna/NC_000964.fna
	cp /var/ngs/bowtie_indexes/bowtie_indexes/SMALL_RNA_GFF_Bsubt168.gff /var/www/jbrowse/Mirjam_Boonstra/docs/gff/SMALL_RNA_GFF_Bsubt168.gff

# change header to >NC_xxx if not done yet
bin/prepare-refseqs.pl --fasta docs/fna/NC_000964.fna	

# add annotation
bin/flatfile-to-json.pl --gff docs/gff/SMALL_RNA_GFF_Bsubt168.gff --trackLabel Original_Annotation --trackType CanvasFeatures

# make feature searchable
bin/prepare-refseqs.pl -gff docs/gff/SMALL_RNA_GFF_Bsubt168.gff

# active the names
bin/generate-names.pl

# make link in the /data folder to the data folder
ln -s /home/anne/PROJECTS/mirjam/2016_03 dataset01
ln -s /home/anne/PROJECTS/mirjam/2017_03 dataset2017_03



# make data/tracks.conf file
# usefull tool is to convert a table direct to a tracks.conf file.
# goto /data and run:
/usr/molgentools/tools/jbrowse_table_2_tracks.pl -i tracks_conf.table > tracks.conf

# Change default spacing between tracks open jbrowse.conf and add the line "view.trackPadding = 7"