Introduction to genome browsers

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• Genome browsers allow us to interpret and view many different types of data associated with genomic positions. They are designed to be used by researchers without programming experience.
• Genome browsers rely on a common reference genome for each species to map data to the correct location.

Data used in this workshop

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• The NTRK2 gene is a useful example for exploring cell-type specific transcript expression.

UCSC Genome Browser: Setup

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• The UCSC genome browser can be easily configured according to your visual preferences and data needs

UCSC Genome Browser: Understanding gene models

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• The UCSC genome browser graphically represents key elements of gene transcripts, including exons, introns, and untranslated regions
• Different settings and tools can be used to configure the browser to more easily investigate specific features of a gene.

UCSC Genome Browser: BLAT tool

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• We can use the UCSC BLAT tool to identify region(s) of similarity between a sequence of interest and other parts of the genome.

UCSC Genome Browser: Gene expression data

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• The UCSC genome browser allows you to compare gene expression data from multiple different sources and species

IGV

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• IGV can sort and index BAM files without use of the command line
• Sorted and indexed BAM files can then be opened to view genomic sequencing and gene expression data in IGV