1. Accessing and visualizing genomics data
Jim Noonan
GENE 760

2. A working definition of genomics
The global study of how biological information is encoded in
genome sequence
Genes
Regulatory sequences
Genetic variation
How this information is read out to produce distinct biological
outcomes
Gene expression and regulation
Cellular identity, differentiation and development
Phenotypic variation among individuals and species

3. Genomes are vast information repositories
Human 3 Gb
kb = 1000 bp
Mb = 1x106 bp
Gb = 1x109 bp
Tb = 1x1012 bp
Pb = 1x1015 bp
1 Gb
10 Gb
100 Gb

4. Sequencing the reference human genome (1990-present; ‘finished’ 2003)
Industrialization of Sanger sequencing,
library construction, sample preparation,
analysis, etc.
$3 billion total cost
1 Gb/month at largest centers (2005)
YCGA = 9.6 Tb per month (2011)

5. Reference genomes

6. Genome assembly and annotation
3 Gb
>>109 sequencing reads
36 bp - 1 kb

7. Genome assembly Scaffold_0: 12,865,123 – 12,965-110
Assembly quality criteria:
Accuracy: number of errors
(Human << 1/100,000 bp)
Contiguity: number of gaps
(Human: est. 357)
Generate reads
Find overlapping reads
Assemble reads into contigs
contig
Coverage:
Average number of reads representing a
particular position in the assembly
Human, Mouse, Rat: > 20x
Chimpanzee: ~6x
Squirrel: ~2x
Join contigs into
scaffolds
scaffold
mate pair
Scaffold_0: 12,865,123 – 12,
Join scaffolds into
“finished” sequence
anchored on chromosomes
AGTTGTATTATTAGAAACTGAGGGCTAAAAACTGTGCACATACACAGACACACATATTATTTTAATATAGATTTTCAATAATTGGTCTAGGATAAGGATAATATACAG
Chr5: 133,876,119 – 134,876,119 7

8. ATATCATGCTTGTCATTCGTTTATCAGAGGCCAAATGTTTTTCTTTGTAAACGTGTGTAAAACATTCTCAGAATTTTAAACAATAACAAATCAGGGCTGAATGTGGCCAACATGCAAAGAGGAAATCTCCCATCTGTCCAAATCAAACAGTTGTATTATTAGAAACTGAGGGCTAAAAACTGTGCACATACACAGACACACATATTATTTTAATATAGATTTTCAATAATTGGTCTAGGATAAGGATAATATACAGAGAACATGCCAAAAGTTTAAGCAAGAAGAAAACAAAGACTGTTACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTAGAAAGACAATGAAACAGAGCCATGTGACCAATGAGAGAGATGAGGGTGGCAGCAGCCTGTTTTAGATAAGGTACCTGATTGGTGGGATTGGAAGACCTCTCTGAGATTAGTGTCTTCAGATATGCCTTAATGATATGAAAGAACCATTCATGGGAAGGCCTAGCATTAAAAACCGTCTAGGCAGAATGAGCAGCAAGTGCAAGGGTCCTGGATAGGAATGAGCTGGATATACTCAAGGAAGAAAGAGAAACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTATCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCAACATGCAAAGAGGAAATCTCCATATCATGCTTGTCATTCGTTTATCAGAGGCCAAATGTTTTTCTTTGTAAACGTGTGTAAAACATTCTCAGAATTTTAAACAATAACAAATCAGGGCTGAATGTGGCCAACATGCAAAGAGGAAATCTCCCATCTGTCCAAATCAAACAGTTGTATTATTAGAAACTGAGGGCTAAAAACTGTGCACATACACAGACACACATATTATTTTAATATAGATTTTCAATAATTGGTCTAGGATAAGGATAATATACAGAGAACATGCCAAAAGTTTAAGCAAGAAGAAAACAAAGACTGTTACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTAGAAAGACAATGAAACAGAGCCATGTGACCAATGAGAGAGATGAGGGTGGCAGCAGCCTGTTTTAGATAAGGTACCTGATTGGTGGGATTGGAAGACCTCTCTGAGATTAGTGTCTTCAGATATGCCTTAATGATATGAAAGAACCATTCATGGGAAGGCCTAGCATTAAAAACCGTCTAGGCAGAATGAGCAGCAAGTGCAAGGGTCCTGGATAGGAATGAGCTGGATATACTCAAGGAAGAAAGAGAAACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTATCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCAACATGCAAAGAGGAAATCTCCATATCATGCTTGTCATTCGTTTATCAGAGGCCAAATGTTTTTCTTTGTAAACGTGTGTAAAACATTCTCAGAATTTTAAACAATAACAAATCAGGGCTGAATGTGGCCAACATGCAAAGAGGAAATCTCCCATCTGTCCAAATCAAACAGTTGTATTATTAGAAACTGAGGGCTAAAAACTGTGCACATACACAGACACACATATTATTTTAATATAGATTTTCAATAATTGGTCTAGGATAAGGATAATATACAGAGAACATGCCAAAAGTTTAAGCAAGAAGAAAACAAAGACTGTTACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTAGAAAGACAATGAAACAGAGCCATGTGACCAATGAGAGAGATGAGGGTGGCAGCAGCCTGTTTTAGATAAGGTACCTGATTGGTGGGATTGGAAGACCTCTCTGAGATTAGTGTCTTCAGATATGCCTTAATGATATGAAAGAACCATTCATGGGAAGGCCTAGCATTAAAAACCGTCTAGGCAGAATGAGCAGCAAGTGCAAGGGTCCTGGATAGGAATGAGCTGGATATACTCAAGGAAGAAAGAGAAACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTATCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCAACATGCAAAGAGGAAATCTCCATATCATGCTTGTCATTCGTTTATCAGAGGCCAAATGTTTTTCTTTGTAAACGTGTGTAAAACATTCTCAGAATTTTAAACAATAACAAATCAGGGCTGAATGTGGCCAACATGCAAAGAGGAAATCTCCCATCTGTCCAAATCAAACAGTTGTATTATTAGAAACTGAGGGCTAAAAACTGTGCACATACACAGACACACATATTATTTTAATATAGATTTTCAATAATTGGTCTAGGATAAGGATAATATACAGAGAACATGCCAAAAGTTTAAGCAAGAAGAAAACAAAGACTGTTACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTAGAAAGACAATGAAACAGAGCCATGTGACCAATGAGAGAGATGAGGGTGGCAGCAGCCTGTTTTAGATAAGGTACCTGATTGGTGGGATTGGAAGACCTCTCTGAGATTAGTGTCTTCAGATATGCCTTAATGATATGAAAGAACCATTCATGGGAAGGCCTAGCATTAAAAACCGTCTAGGCAGAATGAGCAGCAAGTGCAAGGGTCCTGGATAGGAATGAGCTGGATATACTCAAGGAAGAAAGAGAAACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTATCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCAACATGCAAAGAGGAAATCTCC

9. Genome annotation Genes: Genetic variation: Sequence conservation
Coding, noncoding, miRNA, etc.
Isoforms
Expression
~3 billion bp
ACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTAGAAAGACAATGAAACAGAGCCATGTGACCAATGAGAGAGATGAGGGTGGCAGCAGCCTGTTTTAGATAAGGTACCTGATTGGTGGGATTGGAAGACCTCTCTGAGATTAGTGTCTTCAGATATGCCTTAATGATATGAAAGAACCATTCATGGGAAGGCCTAGCATTAAAAACCGTCTAGGCAGAATGAGCAGCAAGTGCAAGGGTCCTGGATAGGAATGAGCTGGATATACTCAAGGAAGAAAGAGAAACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACTAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTACTATGGAAAAATGAAAATAGATTTTAAAACATGTTAATTCACGTTACTTTTTGTTAAATTTACTTTTCTTCTTTCACTTCTTACCTGTCAATGTTATTAATATTTTTAGGAACAATAAATCACATTAATTCCTTATCTCATGTGAAATTTCATATTTATGATTGATACCTTTAAATGTCATTTGTTGAAGGAAGATTATTCATTTTTTCATTCAATAAATATTTTTTAGAATAATAAGTCCCAGGCACAAGACCAGTATTATGTTCTAGGCATTGGGGATACCATGTTCACAAGACAGACTATGATTTACAGGATCAGATGTGGACTCTCAAATTCGACTGAGAATAAAACAGACACAAACAAGTAAATAAAGTTAATTTCAAGTTGTAATTGATGCTATCCCAGGCACAAGACCA….
Genetic variation:
SNPs and CNVs
Sequence conservation
Regulatory sequences:
Promoters
Enhancers
Insulators
Epigenetics:
DNA methylation
Chromatin

10. Density of biological information in the human genome
Chr5: 133,876,119 – 134,876,119
Genes
Transcription
TF binding
Histone mods
Mouse
orthology
SNPs
Repeats

11. Annotation depth varies by species
Human, Mouse (Fly, Worm, Yeast):
Chromosome assemblies
Dense gene and regulatory maps, variation, etc.
Other models (Dog, Chicken, Zebrafish):
Chromosome assemblies
Partial gene maps; variation; little regulatory data
Low coverage vertebrate genomes:
Scaffold assemblies
Few annotated genes
Used for comparative purposes

12. Portals to access and interpret genomes
UCSC Genome Browser (genome.ucsc.edu):
Visualization, data recovery, simple analysis
(also
ENSEMBL (ensembl.org):
Visualization, data recovery, simple analysis
Integrative Genomics Viewer (broadinstitute.orgsoftware/igv/):
Local genome viewer (visualize local and remote data)
Galaxy (main.g2.bx.psu.edu):
Complex data analysis and workflows

13. UCSC Genome Browser
genome.ucsc.edu
Wiki Page: genomewiki.ucsc.edu

14. Read the User Guide

15. Human genome main page (Feb 2009 assembly)
There are multiple assemblies
for many genomes!
Different genome assemblies have different coordinate systems and may have different annotations:
chr2:236,438, ,438,948 in March 2006 (hg18) is chr2:236,773, ,774,209 in Feb 2009 (hg19)

16. Categories of data: displayed as tracks
Genome Viewer
Categories of data: displayed as tracks
Discrete intervals (genes) or continuous
(transcription)
Category: Genes and Gene Prediction
Hyperlinks and tabs for individual tracks
Go to track description page
Hide or show data in genome viewer
Some tracks include multiple datasets (‘subtracks’)
Go to track description page to select
Different assemblies have different
annotations!

17. Sample Genome Viewer image: PITX1
Base position
Gene model (discrete)
Transcription (continuous)
TF binding
SNPs
Repeats

18. Which gene annotation to use?

19. Gene description page and links to other resources

20. ‘Layered’ tracks: Transcription
Display options
Subtracks

21. Integrating different types of annotation data

22. Integrating different types of annotation data
Proximal
enhancer
Promoter

23. Common Genome Browser file formats
BED format
For interval data (e.g., exons)
Tab-delimited format: chr start stop identifier
BED coordinates are ‘zero-based, half-open’: the start position is 0-based,
the end position is 1-based
Position coordinates on the browser are 1-based. This leads to confusion if
you are not careful.
chr is shown in the browser as chr16:
BEDTools: utilities for comparing genomic features you will use on your problem sets
WIG format
For continuous data (e.g., the Transcriptome track mentioned earlier)
WIG files are very large! BigWig is an alternative format you will
learn about in discussion.

24. The Table Browser (under Tools) Select datasets Compare datasets
Download data

25. Integrating your own experimental data
Proximal
enhancer
Promoter
Mapping binding sites for a transcription factor of interest

26. Custom tracks and sessions
Display and share your own data on the browser
Custom tracks can be intersected, etc. in the Table Browser

28. Track Hubs
(under My Data)

29. Integrating Track Hub data with your own experimental data

30. Genome Browser utilities: BLAT
(under Tools)
Rapidly find sequence locations in an assembly
DNA sequences >24 bp and 95% identical to target genome

31. Assembly quality and annotation vary across genomes
Assembly not anchored to
chromosomes
Poor gene annotation
Assembly quality metrics
Whole-genome alignment to
mouse

32. Genome Browser utilities: LiftOver
(under Tools)
Convert coordinates from one assembly to another (e.g., hg18 to hg19)
Identify orthologous positions between genomes (e.g., human to mouse)

33. Galaxy
main.g2.bx.psu.edu

34. Wrap-up
Problem Set #1: Learn how access and manipulate genomic datasets
Next lecture: High-throughput sequencing technologies