igv on cluster - tufts university · viewing the igv window if the genome browser is cut off by...

Start IGV on the Tufts HPC cluster• Using Chrome web browser, log in to ondemand.tufts.edu• Choose Interactive Apps->IGV• Choose desired time, >2 cores, 64 Gb memory• Click “Launch NoVNC” when it appears

Viewing the IGV windowIf the genome browser is cut off by the “Workspace” bar at the bottom -> Resize window using Chrome Zoom options

BAM Visualization with IGVChrom web browser to ondemand.tufts.edu -> login.Choose Interactive Apps->IGVClick “Launch NoVNC” when it appears

RNAseq PreferencesIf you are loading spliced RNAseq BAM files1. Go to View->Preferences

2. Click Alignments -> Track Display Preferences Options3. Check Splice Junction Track. 4. Click "OK"

Load Reference GenomeChoose reference genome by clicking “Genomes” on the top menu

• If you have mapped using a standard reference genome: Choose “Load Genome from Server” and highlight the genome you’d like to download. Leave “Download Sequence” unchecked

• If you mapped using a custom genome:Choose “Load Genome from File” and navigate to the genome location on the cluster. Note that the genome must be indexed e.g. with samtools prior to loading

Load BAMChoose BAM file by clicking on “File” on the top menu

• Navigate to the BAM location on the cluster.• Note that your BAM file must be sorted and

indexed e.g. by samtools

Type gene/contig name here (e.g. SUS1) or coordinates e.g. chrII:400,000-500,000

Zoom in and out

Select a region here to zoom

Splice junctions

BAM Visualization with IGV