# working folder
cd /var/www/jbrowse/Elrike_2018_01
	
# Copy a template folder	

# empty the folder docs/fna
# empty the folder docs/gff
# empty the folder data/bed
# 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
	copy all bed to ./data/bed
	
FNA=docs/fna/PG10.fna
GFF=docs/gff/PG10from168.gff3

		

# change header to one ID: e.g. >NC_000964.3	
bin/prepare-refseqs.pl --fasta $FNA

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



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

# add promoter data from TSSer
bin/flatfile-to-json.pl --bed docs/bed/TSSer.bed --trackType CanvasFeatures --trackLabel TSSerAll
bin/flatfile-to-json.pl --bed docs/bed/TSSer_100.bed --trackType CanvasFeatures --trackLabel TSSer_100
bin/flatfile-to-json.pl --bed docs/bed/RiboSwitch.bed --trackType CanvasFeatures --trackLabel RiboSwitch
bin/flatfile-to-json.pl --bed docs/bed/TSSer_pDSM2542-1.bed --trackType CanvasFeatures --trackLabel TSSer_pDSM2542-1
bin/flatfile-to-json.pl --bed docs/bed/TSSer_pDSM2542-2.bed --trackType CanvasFeatures --trackLabel TSSer_pDSM2542-2


# 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 /data/home/anne/PROJECTS/Elrike/2016-12 data01
	ln -s /data/home/anne/PROJECTS/Elrike/2016-06/results_2018Jan18 data02


# 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

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

# Optional BAM files:
# 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



http://jbrowse.molgenrug.nl/Elrike_2016_12/?loc=NZ_CP012712.1%3A1744062..1744131&tracks=DNA%2COriginal_Annotation%2Cbigwig-track_001_plus%2Cbigwig-track_001_zmin%2Cbigwig-track_002_plus%2Cbigwig-track_002_zmin%2Cbigwig-track_003_plus%2Cbigwig-track_003_zmin&highlight=