IGV Genome Browser

Templates

for d in img js css;do
    [ -d "templates/igv/$d" ] || mkdir -p "templates/igv/$d"
done
wget -O templates/igv/img/favicon.ico 'https://igv.org/web/img/favicon.ico'
wget -O templates/igv/js/igv.min.js 'https://igv.org/web/release/2.1.0/dist/igv.min.js'
wget -O templates/igv/css/bootstrap.min.css 'https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css'
wget -O templates/igv/js/bootstrap.min.js 'https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js'
wget -O templates/igv/js/jquery-3.2.1.slim.min.js 'https://code.jquery.com/jquery-3.2.1.slim.min.js'
wget -O templates/igv/js/popper.min.js 'https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js'

Genome reference from IGV

wget -O genome/hg38/source/igv.hg38.genome http://s3.amazonaws.com/igv.broadinstitute.org/genomes/hg38.genome
unzip genome/hg38/source/igv.hg38.genome -d genome/hg38/igv

Generate IGV html

IGV Browser reference

igv.browser

addMultiLocusPanelWithGenomicStateAtIndex: ƒ (genomicState,index,viewportWidth) addTrack: ƒ (track) buildViewportsWithGenomicStateList: ƒ (genomicStateList) cancelTrackPan: ƒ () compressedSession: ƒ () dispose: ƒ () emptyViewportContainers: ƒ () endTrackDrag: ƒ () findTracks: ƒ (property,value) fireEvent: ƒ (eventName,args,thisObj) getChromosomeLengthBP: ƒ (genome,referenceFrame) goto: ƒ (chrName,start,end) hideCenterGuide: ƒ () hideCursorGuide: ƒ () hideTrackLabels: ƒ () isMultiLocusMode: ƒ () isMultiLocusWholeGenomeView: ƒ () loadGenome: ƒ (idOrConfig,initialLocus) loadInProgress: ƒ () loadSampleInformation: ƒ (url) loadSession: ƒ (sessionURL,config) loadTrack: ƒ (config) loadTrackList: ƒ (configList) minimumBases: ƒ () mouseDownOnViewport: ƒ (e,viewport) on: ƒ (eventName,fn) presentAlert: ƒ (alert,$parent,callback) presentMessageWithCallback: ƒ (message,callback) presentSplitScreenMultiLocusPanel: ƒ (alignment,genomicState) removeAllTracks: ƒ (removeSequence) removeMultiLocusPanelWithGenomicState: ƒ (genomicState,doResize) removeTrack: ƒ (track) removeTrackByName: ƒ (name) renderSVG: ƒ (config) reorderTracks: ƒ () resize: ƒ () search: ƒ (string,init) selectMultiLocusPanelWithGenomicState: ƒ (selectedGenomicState) sessionURL: ƒ () setTrackHeight: ƒ (newHeight) setTrackLabelName: ƒ (trackView,name) showCenterGuide: ƒ () showCursorGuide: ƒ () showTrackLabels: ƒ () startTrackDrag: ƒ (trackView) toJSON: ƒ () un: ƒ (eventName,fn) updateLocusSearchWidget: ƒ (genomicState) updateTrackDrag: ƒ (dragDestination) updateUIWithGenomicStateListChange: ƒ (genomicStateList) updateViews: ƒ (genomicState,views) updateZoomSlider: ƒ ($slider) viewportContainerWidth: ƒ () viewportWidth: ƒ () visibilityChange: ƒ () zoom: ƒ (scaleFactor) zoomIn: ƒ () zoomOut: ƒ () zoomWithRangePercentage: ƒ (percentage) zoomWithScaleFactor: ƒ (centerBPOrUndefined,viewportOrUndefined,scaleFactor)

File extensions

narrowpeak
broadpeak
peaks
bedgraph
wig
gff3
gff
gtf
fusionjuncspan
refflat
seg
aed
bed
vcf
bb
bigbed
bw
bigwig
bam
tdf
refgene
genepred
genepredext
bedpe
bp
snp
rmsk

Track configuration reference

track1:
    type: wig
    format: bigwig
    height: 200
    min: 0
    max: 100
    color: 'rgb(0,0,0)'
    autoScale: true,
    logScale: false

long_RNA:
    url: genome/hg38/genePred/long_RNA.genePred
    type: annotation
    format: genepred
    height: 200

{
    echo 'reference:
    id: hg38
    fastaURL: genome/hg38/fasta/genome.fa
    indexURL: genome/hg38/fasta/genome.fa.fai
    cytobandURL: genome/hg38/igv/cytoBandIdeo.txt
Refseq Genes:
    type: annotation
    format: refGene
    url: genome/hg38/igv/refGene.txt
    visibilityWindow: 300000000
    height: 80
GENCODE_V27:
    type: annotation
    format: bed
    url: genome/hg38/igv/gencode.bed
    indexURL: genome/hg38/igv/gencode.bed.idx
    displayMode: "EXPANDED"
    searchable: true
    visibilityWindow: 300000000
    height: 200'
    for sample_id in $(head -n 50 data/scirep/sample_ids.txt);do
        printf "${sample_id}(+):
    url: scirep/${sample_id}.transcriptome.+.bigWig
    type: wig
    format: bigwig
    height: 25
${sample_id}(-):
    url: scirep/${sample_id}.transcriptome.-.bigWig
    type: wig
    format: bigwig
    height: 25
"
    done
} > genome_browser/config/scirep.yaml
bin/create_igv.py -i templates/igv/main.html -g hg38 \
    --tracklist genome_browser/config/scirep.yaml \
    --base-url http://166.111.156.12:10080/genomebrowse \
    -o genome_browser/igv/scirep.html
sync-bigwig

bin/create_igv.py -i templates/igv/main.html -g hg38 --genome-dir genome/hg38/ \
    --track genome/hg38/bed/long_RNA.intron.bed \
    --track genome/hg38/bed/rmsk.bed \
    --track genome/hg38/bed/promoter.merged.bed \
    --track genome/hg38/bed/enhancer.merged.bed \
    --track output/scirep/bigwig/Sample_1S1.genome.+.bigWig \
    --track output/scirep/bigwig/Sample_1S1.genome.-.bigWig \
    -o igv.html

bin/create_igv.py -i templates/igv/main.html -g hg38 --genome-dir genome/hg38/ \
    --tracklist tmp/tracklist.yaml \
    -o igv.html
--track output/scirep/bigwig/Sample_1S1.genome.+.bigWig -o igv.html

Reference tracks

gtfToGenePred -geneNameAsName2 -genePredExt genome/hg38/gtf/gencode.gtf genome/hg38/genePred/gencode.genePredExt
gffread -E --bed genome/hg38/gtf/gencode.gtf -o /dev/stdout | bedtools sort > genome/hg38/igv/gencode.bed
./tools/IGVTools/igvtools index genome/hg38/igv/gencode.bed

Domains

gffread --bed -o genome/hg38/bed/long_RNA.bed genome/hg38/gtf/long_RNA.gtf
gffread --bed -o genome/hg38/bed/gencode_tRNA.bed genome/hg38/gtf/gencode_tRNA.gtf

[ -d "output/scirep/gdomains/20/05.bed" ] || mkdir -p output/scirep/gdomains/20
{
    bin/tbed2gbed <(cat genome/hg38/bed/long_RNA.bed genome/hg38/bed/gencode_tRNA.bed) <(grep -v '^chr' output/scirep/domains/20/05.bed) /dev/stdout
    awk 'BEGIN{OFS="\t";FS="\t"}/^chr/{print $0,0,0,0,1,$3-$2,0}' output/scirep/domains/20/05.bed
} | bedtools sort > output/scirep/gdomains/20/05.bed

Custom reference genome

IGV genome repository: (https://s3.amazonaws.com/igv.org.genomes/genomes.json)
Cytoband schema: UCSC

genome="rRNA"
fastaURL="genome/hg38/fasta/${genome}.fa"
fastaIndexURL="genome/hg38/fasta/${genome}.fa.fai"
cytobandURL="genome/hg38/cytoband/${genome}.txt"
refURL="genome/hg38/genePred/${genome}.genePred"
# convert NR_ ids to rRNA names
# gene_id|gene_name
rRNAIdFile="genome/hg38/source/refSeq_rRNA.ids.txt"

awk 'BEGIN{OFS="\t";FS="\t"}{print $1,0,$2,"p"NR".1","gneg"}' "$fastaIndexURL" > "$cytobandURL"
bedToGenePred <(awk 'BEGIN{OFS="\t";FS="\t"}NR==FNR{split($0,a,"|");name[a[1]]=a[2];next}{print $1,0,$2,name[$1],0,"+"}' "$rRNAIdFile" "$fastaIndexURL") "$refURL"

genome="circRNA"
fastaURL="genome/hg38/fasta/${genome}.fa"
fastaIndexURL="genome/hg38/fasta/${genome}.fa.fai"
cytobandURL="genome/hg38/cytoband/${genome}.txt"
refURL="genome/hg38/genePred/${genome}.genePred"

awk 'BEGIN{OFS="\t";FS="\t"}{print $1,0,$2,"p"NR".1","gneg"}' "$fastaIndexURL" > "$cytobandURL"
bedToGenePred <(awk 'BEGIN{OFS="\t";FS="\t"}{print $1,0,$2,$1,0,"+"}' "$fastaIndexURL") "$refURL"

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