IGV; the integrated genome viewer is a widely used tool to navigate genomes. It allows the user to load many datasets, to display them alongside annotation tracks.

• Go to the IGV Web App
• Select the human genome version hg19.
• Navigate to the TIAM2 gene
• How many transcripts NM* have been characterised in RefSeq for this gene?

Sequencing data

• Load the reads and their index file as tracks
• Navigate to the region 104,292,390-104,292,760 of chromosome 9
• Show reads in pairs, colour them by read strand
• Determine the coordinates of the deletion; is this deletion rare?
• Using SNPedia, check if any of the SNP in the region has been involved in a human pathology

Based on some ideas borrowed from this IGV tutorial. The dataset is based on the BH01 data provided by Snyder et al. Cell 2016.