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.
- 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
- 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)