Exploring genome features with the UCSC Genome Browser

Bingbing Yuan

BaRC Hot Topics – April 14, 2015

Bioinformatics and Research Computing

Whitehead Institute

http://barc.wi.mit.edu/hot_topics/ 1

Why UCSC Genome Browser ?

• Visualize many datasets hosted in UCSC

• Visualize your genome-mapped datasets

• Download genome features with the Table Browser

2

Today’s outline

• Introduction to the genome view and track display • Search and display ENCODE data • View your list of regions in the browser • Use table browser to download and annotate genome

features • Convert coordinates/features between genomes • Use Public Hub to display tracks hosted at non-UCSC

servers. • Save your session

Throughout the talk: mining the genome content

3

UCSC Genome Browser http://genome.ucsc.edu

Local: http://membrane.wi.mit.edu/

4

Global View

5

Genome Viewer

Tracks (group of data)

Navigation

6

Click: item description

Clic

k: t

rack

de

scri

pti

on

R

igh

t cl

ick:

tra

ck c

on

figu

rati

on

Drag track to new position

Zoom in with Drag-and-select

7

Track description

8

Item description

9

configure

10

11

mode of an individual annotation track: Hide: the track is not displayed at all.

Dense: the track is displayed with all features collapsed into a single line.

Squish: the track is displayed with each annotation feature shown separately, but at 50% the height of full mode. Features are unlabeled.

Pack: the track is displayed with each annotation feature shown separately and labeled

Full: the track is displayed with each annotation feature on a separate line.

Gene structure

12

5’UTR 3’UTR Coding exon

Intron

Commonly used gene models GENCODE, Ensembl, UCSC, Refseq

View genes/exons only

13

multi-region

Browser Tracks

click links for detail information

14

The current genome build might have less tracks than the last version. For example: hg38 has considerably fewer tracks than hg19

Demo and Exercise 1

• Search your favorite gene in the genome browser.

• How many exons does your gene have? What’s the strand orientation relative to the genome?

• How many isoforms does this gene have?

• Does the RefSeq gene catalog contain the correct number of isoforms of your favorite human gene?

• Zoom in to look for the start codon. You may need to change the track setting.

15

ENCODE super track settings

16

ENCODE track setting

17

ENCODE: genome.ucsc.edu/ENCODE/

18

ENCODE: search tracks

19

Demo and Exercise 2

• Identify the transcription factor binding sites in your gene’s promoter region.

• Are there any RNA-seq data expressed in your favorite cell/tissue? If so, which isoform is most likely to be expressed?

20

Add custom track

21

OR

track name='sample peaks' description='sample peaks'

track name='User Track' description='User Supplied Track'

File format: above links Or view in

http://genome.ucsc.edu/FAQ/FAQformat.html

WI UCSC Browser: membrane.wi.mit.edu URL for viewing files: http://tak.wi.mit.edu/solexa_ucsc/

URL

File Formats

22

Bed: regions Enriched Chip-seq signal for TF binding

Wig(gle): continues signal Chip-seq signal

BAM: alignment of reads RNA-seq alignment

23

UCSC Table Browser

Demo and exercise 3

• Load peaks (bed format) derived from Chip-seq: • GM12878 H3K36me3 Histone Mods by ChIP-seq Peaks

from ENCODE/Broad

• To save time, only peaks in chr22

• Identify the Refseq genes that could be regulated by H3K36me3 – Go to the Table Browser:

– Choose RefGene table

– Intersect with the above uploaded track

24

Convert to other genome/build

25

Save to file

Convert to other genome/build LiftOver: multiple regions

26

blat: align sequences

27

view alignment in browser

Track Data Hubs

28

Share/save session

29

More Information

• UCSC Browser Tutorials https://genome.ucsc.edu/training/index.html

Free Videos:

https://genome.ucsc.edu/training/vids/index.html

Open Helix:

http://www.openhelix.com/ucsc

• FAQ: https://genome.ucsc.edu/FAQ/

• Genomewiki: http://genomewiki.ucsc.edu/index.php/Main_Page

30