JBrowse

folder structure

1. folder raw data: /var/www/html/jbrowse/sample_data/raw/
2. folder configuration files: /var/www/html/jbrowse/sample_data/json/

We have to create a new folder for each dataset:

mkdir /var/www/html/jbrowse/sample_data/raw/MTB
mkdir /var/www/html/jbrowse/sample_data/json/MTB

Add reference from fasta

cd /var/www/html/jbrowse/sample_data/json/MTB
prepare-refseqs.pl --fasta NC_000962.fna

• This will create
  • /var/www/html/jbrowse/sample_data/json/MTB/tracks.conf
  • /var/www/html/jbrowse/sample_data/json/MTB/trackList.json
  • /var/www/html/jbrowse/sample_data/json/MTB/seq

Add bam track files

• Add sorted bam file in "/var/www/html/jbrowse/sample_data/raw/MTB"
• Index bam file

cd /var/www/html/jbrowse/sample_data/raw/MTB
samtools index 538048.bam

• Add bam track to tracks.conf

emacs -nw /var/www/html/jbrowse/sample_data/json/MTB/tracks.conf

Content:

# make a section for the new track called tracks.(unique name)
[ tracks.my-bam-track ]

# settings for what data is shown in the track
storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = ../../raw/MTB/538048.bam
baiUrlTemplate = ../../raw/MTB/538048.bam.bai

type = JBrowse/View/Track/Alignments2
key  = BAM alignments from sample XYZ
renderPrettyAlignments = true

[ tracks.bam-coverage ]

storeClass     = JBrowse/Store/SeqFeature/BAM
urlTemplate    = ../../raw/MTB/538048.bam
baiUrlTemplate = ../../raw/MTB/538048.bam.bai

type = JBrowse/View/Track/SNPCoverage

Add gene track

# convert gbk to gff
gbk2gff.py -i genome_gbwithparts.gbk -o genome_gbwithparts.gff

# add track
flatfile-to-json.pl --gff genome_gbwithparts.gff --type CDS --trackLabel ORFs --out /var/www/html/jbrowse/sample_data/json/MTB --nameAttributes locus_tag

Add locus tags index

cd /var/www/html/jbrowse/sample_data/raw/MTB
generate-names.pl --verbose --out /var/www/html/jbrowse/sample_data/json/MTB

This will create

• /var/www/html/jbrowse/sample_data/json/MTB/names

Access browser

http://127.0.0.1/jbrowse/index.html?data=sample_data/json/MTB