# working folder
	/var/www/jbrowse/Sjoerd-MS2

# empty the folder docs/fna
# empty the folder docs/gff
# empty the folder data/names
# empty the folder data/seq	
# empty the folder data/tracks	

# format refseq 
	copy all fna to ./docs/fna
	copy all gff to ./docs/gff

# change header to one ID: >NC_000964.3	
bin/prepare-refseqs.pl --fasta docs/fna/MG1363_2016Feb.fna	

# add annotation
bin/flatfile-to-json.pl --gff docs/gff/MG1363_ncRNA_2016Feb.gff --trackLabel Original_Annotation --trackType CanvasFeatures



# make feature searchable
# bin/prepare-refseqs.pl -gff docs/gff/xxxxx.gff
bin/prepare-refseqs.pl -gff docs/gff/MG1363_ncRNA_2016Feb.gff


# active the names
bin/generate-names.pl

# make link to the /data folder
	# 2016-06  reanalysis of all data, make new link
	cd ./data
	ln -s /home/anne/PROJECTS/sjoerd/2016-08-PrimBio dataset


# make data/tracks.conf file
# usefull tool is to convert a table direct to a tracks.conf file.
# goto /data and run:
cd ./data
/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"

# 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