Circular View
This page describes the integration of the IGV-Web app with the JBrowse 2 circular view component, for exploring structural variants, chromatin interactions, and other long-distance interactions. Currently this integration supports structural variants from VCF files, paired and split-read alignments from BAM/CRAM files, and interaction pairs from bedPE and interact tracks.
Example contributed by Chee-Hong Wong of the Wei Lab with data from Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription; Yanfen Zhu, Amit D. Gujar, et. al, Cell 2021; 39; 694-707
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Open https://igv.org/app
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From the Sessions menu select ChIA-Pet - Wei Lab GSM3553630
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Two BEDPE files are loaded. They are large and may take a few seconds to load. The top track contains inter-chromosomal interactions. The bottom track contains intra-chromosomal interactions. Using the IGV multi-locus view, the tracks are split into three panels at loci of interest on chromosomes 7, 8, and 12.
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Select Show from the Circular View menu. This will open the circular view window.
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Right-click over the rightmost panel in the Trans Interactions track, which displays a region on chromosome 12. Select Add interactions to circular view to display chords in the circular view that represent the interactions seen in that region. The chords are drawn in the grey color representing chromosome 12.
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Repeat for the other two panels (chr7 and chr8). The chords will be drawn in light blue and maroon for chromosomes 7 and 8, respectively.
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Click Show Controls on the circular view window. Use sliders to adjust transparency of each chord set
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Select Clear All from the circular view window.
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To focus on dominant signals, click the gear icon
for the Trans Interactions
track and select Set data range. Set the Minimum threshold to 9 in the window that pops up.
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From the gear menu select Add interactions to circular view to add interactions from all panels.
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Repeat for the Cis Interactions track.
Data courtesy of the Schatz Lab. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of the SKBR3 breast cancer cell line, Nattestad et al. (2017) Genome Research doi: 10.1101/gr.231100.117.
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Open https://igv.org/app
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From the Sessions menu select SKBR3 - Illumina (Schatz)
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The session loads two tracks. The top track Translocations (Delly) contains structural variant calls from a VCF file; the second track contains paired-end alignments from a BAM file. The alignments are color-coded by the chromosomes of the mates; pairs where both reads align to the same chromosome are grey.
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Select Show from the Circular View menu. This will open the circular view window.
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Right click over the Alignments track and select Add discordant pairs to circular view.
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Click on the chords in the circular view to see connecting regions in IGV's multi-locus view.
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From the Sessions menu select SKBR3 - Pacbio (Schatz). Note: This is a large and unusually deep coverage long-read dataset. It takes some time to load.
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The session loads two tracks. The top track Translocations (Sniffles) contains structural variant calls from a VCF file; the second track contains long-read (Pacbio) alignments from a BAM file. The multicolor alignment blocks are "soft clips".
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The session loads two tracks. The top track Translocations (Sniffles) contains structural variant calls from a VCF file; the second track contains long-read (Pacbio) alignments from a BAM file. The multicolor alignment blocks are "soft clips".
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Select Show from the Circular View menu. This will open the circular view window.
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Right click over the Alignments track and select Add split reads to circular view.
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Click on the chords in the circular view to see connecting regions in IGV's multi-locus view.
