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Multi-Region trilogy part 2: Viewing alternate haplotypes with the UCSC Genome Browser

Difficulty level
Beginner
Duration
7:04
Topic

This tutorial demonstrates viewing alternate haplotypes with the UCSC Genome Browser.

Topics covered in this lesson
  • Set up the Genome Browser display
  • View alternate sequences
  • Fetch sequence of right end of alt
  • Fetch sequence of left end of alt
  • Blat the alt ends
  • Substitute alt ends into chromosome
  • Track lifted from hg19 lacks hg38 annotations on alt
  • Remove alt from main chromosome
Prerequisites

Tutorial: Multi-Region trilogy part 1: Exon-only display in the UCSC Genome Browser