2.13 Conclusion

In this lab, we explored several of the most commonly used websites in genomics:

2.13.0.1 Genome browsers

  • UCSC genome browser: Used to explore features of the human genome
    • If you discover an interesting SNP in your research, you might look it up in the UCSC browser to see which genes it’s in/near, if it overlaps with any repetitive elements, etc.

  • IGV: Used to visualize sequencing data
    • It’s common practice to look at your sequencing reads in IGV to check alignment quality, verify that SNPs look like real variants and not errors, etc.

2.13.0.2 Data repositories

  • 1000 Genomes Project: One of the largest and most diverse datasets of human sequencing data
    • Data from 1000 Genomes is frequently used in human genetics studies

  • SRA: A repository for publicly available sequencing data
    • Genetics studies deposit their data in SRA if it can be made publicly available (i.e., if it has no identifiable information)