Visualizing ENCODE Data in the UCSC Genome Browser Pauline Fujita, - - PowerPoint PPT Presentation

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Visualizing ENCODE Data in the UCSC Genome Browser Pauline Fujita, - - PowerPoint PPT Presentation

Feb 18, 2024 131 likes •793 views

Visualizing ENCODE Data in the UCSC Genome Browser Pauline Fujita, Ph.D. UCSC Genome Bioinformatics Group Training Resources genome@soe.ucsc.edu Genomewiki: genomewiki.ucsc.edu Mailing list archives: genome.ucsc.edu/FAQ/ Training page:

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Visualizing ENCODE Data in the UCSC Genome Browser

Pauline Fujita, Ph.D.

UCSC Genome Bioinformatics Group

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Training Resources

genome@soe.ucsc.edu

  • Genomewiki: genomewiki.ucsc.edu
  • Mailing list archives:

genome.ucsc.edu/FAQ/

  • Training page:

genome.ucsc.edu/training.html

  • Twitter

@GenomeBrowser

  • Tutorial videos: YouTube channel
  • Open Helix: openhelix.com/ucsc
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Outline

  • Basics: search, display, more info
  • Tools for finding ENCODE data
  • Annotating a BED file: RNAseq example
  • Annotating a VCF file
  • Track Hubs: What are they? How do I

make one?

  • Exercises
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SLIDE 4

Basic Navigation: Main Display

genome.ucsc.edu/cgi-bin/hgTracks?db=hg19

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Display Configuration

  • Visibility:

hide, dense, squish, pack, full

  • Track ordering: drag and drop
  • Drag and zoom/highlighting
  • Configuration page
  • Right click menu
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SLIDE 6

How to find more info

Track Description Item Description

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More info: Track Description

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More info: Item Description

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ENCODE

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ENCODE: Super-track Settings

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ENCODE: Track Settings

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ENCODE: Item Details

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ENCODE Tools

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ENCODE

ENCODE

genome.ucsc.edu/ENCODE/

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ENCODE: Experiment Matrix

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ENCODE: ChIP-Seq Matrix

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ENCODE: Experiment Summary

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ENCODE: Track Search

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A A G G A C T G A A C T C A G G C A G A G T C C A A G A G T C G C A G G A A C CTT T C G A T C T C C T

File Formats

Scale chr2: GM12878 Ht 2 GM12878 Pk 2 2 kb hg19 191,876,000 191,877,000 191,878,000 191,879,000 191,880,000 191,881,000 Basic Gene Annotation Set from GENCODE Version 19 DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington GM12878 DNaseI HS Raw Signal Rep 2 from ENCODE/UW K562 TFBS Uniform Peaks of Znf143_(16618-1-AP) from ENCODE/Stanford/Analysis K562 Znf143 IgG-rab ChIP-seq Peaks from ENCODE/SYDH K562 Znf143 IgG-rab ChIP-seq Signal from ENCODE/SYDH K562 polyA+ IFNa30 RNA-seq Alignments from ENCODE/SYDH Exome Aggregation Consortium (ExAC) - Variants from 60,706 Exomes STAT1 STAT1 STAT1 STAT1 STAT1 A G

  • T

C C T T C G C T GM12878 Sg 2 100 _ 1 _ K562 Z143 IgR 40 _ 3 _

bit.ly/fileformatsession BED

wig(gle)

BAM VCF

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SLIDE 20

Scale chr2: GM12878 Ht 2 GM12878 Pk 2 2 kb 191,876,000 191,877,000 STAT1 STAT1 STAT1 STAT1 STAT1 A G G A A C CTT

  • T

C G A T C C T T C G A A G G A C T G A A C T C A G G C A G A G T C C A A G A G T C G C A G C T T C T C C T GM12878 Sg 2 100 _ 1 _ K562 Z143 IgR 40 _ 3 _

File Formats

hg19 191,878,000 191,879,000 191,880,000 191,881,000 Basic Gene Annotation Set from GENCODE Version 19 DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington GM12878 DNaseI HS Raw Signal Rep 2 from ENCODE/UW K562 TFBS Uniform Peaks of Znf143_(16618-1-AP) from ENCODE/Stanford/Analysis K562 Znf143 IgG-rab ChIP-seq Peaks from ENCODE/SYDH K562 Znf143 IgG-rab ChIP-seq Signal from ENCODE/SYDH K562 polyA+ IFNa30 RNA-seq Alignments from ENCODE/SYDH Exome Aggregation Consortium (ExAC) - Variants from 60,706 Exomes

BED

wig(gle)

BAM VCF

Positional annotations. (ex. Regions w/: enriched ChIP-seq signal for TF binding, Δ’l methylation, splice jxns from RNA-seq) Continuous signal data. # of reads (ex. DNase I HS and ChIP-seq signals) Alignments of seq. reads, mapped to genome (ex. RNA- seq alignments) Variation data: SNPs, indels, Copy Number Variants, Structural Variants (ex. ExAC data)

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SLIDE 21

Scale chr2: GM12878 Ht 2 GM12878 Pk 2 2 kb 191,876,000 191,877,000 STAT1 STAT1 STAT1 STAT1 STAT1 A G G A A C CTT

  • T

C G A T C C T T C G A A G G A C T G A A C T C A G G C A G A G T C C A A G A G T C G C A G C T T C T C C T GM12878 Sg 2 100 _ 1 _ K562 Z143 IgR 40 _ 3 _ DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington K562 Znf143 IgG-rab ChIP-seq Peaks from ENCODE/SYDH K562 polyA+ IFNa30 RNA-seq Alignments from ENCODE/SYDH 191,879,000

Indexed File Formats

191,878,000 Basic Gene Annotation Set from GENCODE Version 19 GM12878 DNaseI HS Raw Signal Rep 2 from ENCODE/UW K562 TFBS Uniform Peaks of Znf143_(16618-1-AP) from ENCODE/Stanford/Analysis K562 Znf143 IgG-rab ChIP-seq Signal from ENCODE/SYDH Exome Aggregation Consortium (ExAC) - Variants from 60,706 Exomes hg19 191,880,000 191,881,000

BED bigBed

wig(gle)

bigWig BAM VCF

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SLIDE 22

Indexed File Formats

  • Only displayed portions of files

transferred to UCSC

  • Display large files (would time out)
  • File + index on your web-accessible

server (http, https, or ftp)

  • Faster display
  • More user control
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File Formats

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File Formats

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File Formats

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File Formats

www.encodeproject.org/help/file-formats/

Help File formats

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Custom Tracks

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Custom Tracks

genome.ucsc.edu/cgi-bin/hgCustom

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Custom Tracks

genome.ucsc.edu/cgi-bin/hgCustom

track name=”BED_custom_track” chr7 127471196 127472363 Gene1

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Annotating your data: BED

Tools

Data Integrator

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Data Integrator

genome.ucsc.edu/cgi-bin/hgIntegrator

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Data Integrator

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Data Integrator

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http://genome.ucsc.edu/cgi-bin/hgIntegrator?hgsid=43297266... 1 of 1 6/26/15, 3:20 PM

Data Integrator

#ct_SYDHTFBS_4733.chrom ct_SYDHTFBS_4733.chromStart ct_SYDHTFBS_4733.chromEnd ct_SYDHTFBS_4733.name ct_SYDHTFBS_4733.score wgEncodeGencodeBasicV19.name wgEncodeGencodeBasicV19.name2 chr21 33031473 33032186 . 608 ENST00000449339.1 AP000253.1 chr21 33031473 33032186 . 608 ENST00000270142.6 SOD1 chr21 33031473 33032186 . 608 ENST00000389995.4 SOD1 chr21 33031473 33032186 . 608 ENST00000470944.1 SOD1

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Annotating your VCF file

  • 1. Make a VCF custom track
  • 2. Go to the Variant Annotation Integrator
  • 3. Choose your track
  • 4. Add annotations
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Remotely Hosted Custom Tracks

  • Put data file (bigBed/bigWig/BAM/VCF, etc)

in internet accessible location

  • Must have: 1. track info, 2. bigDataUrl
  • VCF example:

track type=vcfTabix name="VCF_Example" description="VCF Ex. 1: 1000 Genomes phase 1 interim SNVs" bigDataUrl= http://hgwdev.cse.ucsc.edu/~pauline/presentations/ vcfExample.vcf.gz

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Variant Annotation Integrator

  • Upload pgSnp or VCF custom track
  • Associate UCSC annotations with your

uploaded variant calls

  • Add dbSNP info if dbSNP identifier

found

  • Select custom track and VAI options

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Variant Annotation Integrator

Tools Variant Annotation Integrator

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Variant Annotation Integrator

genome.ucsc.edu/cgi-bin/hgVai

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Track Data Hubs


  • Remotely hosted
  • Data persistence
  • File formats:

bigBED, bigWig, BAM, VCF

  • Track organization:

groups, supertracks

  • multiWigs
  • Assembly hubs
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SLIDE 41

Track Hubs

My Data Track Hubs

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Track Hubs

genome.ucsc.edu/cgi-bin/hgHubConnect

My Data Track Hubs

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My Hubs

genome.ucsc.edu/cgi-bin/hgHubConnect

My Data Track Hubs

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SLIDE 44

Make Your Own Track Hub

You will need:

  • Data (compressed binary index formats:

bigBed, bigWig, BAM, VCF)

  • Text files to define properties of the

track hub

  • Internet-enabled web/ftp server
  • Assembly Hubs:

a twoBit sequence file

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SLIDE 45

Track Hubs

genome.ucsc.edu/cgi-bin/hgHubConnect

My Data Track Hubs

myHub/ - directory containing track hub files hub.txt - a short description of hub properties genomes.txt - list of genome assemblies included hg19/ - directory of data for the hg19 human assembly Data files! BAM, bigBed, bigWig, VCF

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An Example Assembly Hub

An Arabidopsis hub: http://genome-test.cse.ucsc.edu/ ~pauline/hubs/Plants/hub.txt

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Acknowledgements

UCSC Ge UCSC Geno nome me Br Browse wser t r team am

– Da David Hau vid Haussle ssler – co r – co-PI

  • PI

– Jim K im Kent – Br nt – Browse wser Co r Conce ncept, BLA pt, BLAT, T , Team Le am Leade ader, PI , PI – Bo Bob K b Kuhn hn –

– Asso

Associat ciate Dire Direct ctor, Ou , Outre treach – co ach – co-PI

  • PI

– Do Donna K nna Kar arolchik lchik, Ann Z , Ann Zweig – Pr ig – Proje ject Manage ct Manageme ment nt Engine Engineering ring QA QA, Do , Docs, Su cs, Suppo pport t Sys-admins Sys-admins

Angie Hinrichs Katrina Learned Jorge Garcia Pauline Fujita Erich Weiler Kate Rosenbloom Hiram Clawson Luvina Guruvadoo Gary Moro Steve Heitner Galt Barber Brian Raney Brian Lee Max Haeussler Jonathan Caspar Matt Speir

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SLIDE 48

THE GB TEAM

UC Santa Cruz Genomics Institute

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SLIDE 49

Funding Sources

Na Nation tional Huma l Human Gen Genome R

  • me Resea

esearch In h Institut stitute (NHGRI) e (NHGRI) Na Nation tional Ca l Cancer cer In Institut stitute (NCI) e (NCI) Na Nation tional In l Institut stitute f e for

  • r Den

Denta tal a l and d Cr Cranio-F

  • Facia

cial R l Resea esearch (NIDCR) h (NIDCR) Na Nation tional In l Institut stitute f e for

  • r Child Hea

Child Health a lth and Huma d Human De Developmen elopment (NICHD) t (NICHD) QB3 ( QB3 (UCB UCBerkele ley, UCSF , UCSF, UCSC) , UCSC) Amer America ican R Reco ecover ery a y and R d Rein einvestmen estment A t Act (ARRA) stimulus fun ct (ARRA) stimulus funds ds

UC Santa Cruz Genomics Institute

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SLIDE 50

genome.ucsc.edu 


THANK YOU!

UC Santa Cruz Genomics Institute

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Exercises

  • 1. Load example BED and VCF tracks via url
  • 2. Look at custom track data by pasting url into a

web browser.

  • 3. Annotate the TFBS custom track using the Data

Integrator.

  • 4. Annotate the VCF custom track using the Variant

Annotation Integrator.

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Exercise 1

Load example BED and VCF tracks via url

  • 1. Go to the Custom tracks menu
  • My Data -> Custom Tracks
  • 2. Input this url: http://bit.ly/customtracks (note that you

must include the ”http” part of this url or you will get an error) and click [submit].

  • 3. Click the [Go to genome browser] button.
  • 4. Once in the main Browser, jump to this position:
  • chr21:33,034,804-33,037,719
  • 5. See if you can drag your 2 custom tracks to the top of

the display

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SLIDE 53

Exercise 2

Exploring your BED and VCF tracks

  • 1. Now that you have 2 custom tracks loaded, take a look

at the data by pasting that same url into a web browser:

  • 2. These custom tracks are actually data copied from some

existing tracks, see if you can find them, turn them on, and observe that the original tracks and custom tracks look the same in the browser:

  • Track 1 (BED format): Group (Regulation), Super

Track (ENC TF Binding), Track (SYDH TFBS)

  • Track 2 (VCF format): Group (Variation), Track

(1000G Ph1 Vars)

  • 3. Navigate to this position for best comparison (esp. for the

VCF track): chr21:33,034,804-33,037,719

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Exercise 3

Annotate your BED with the Data Integrator

  • 1. Go to the Data Integrator
  • 2. Once there select:
  • 1. Region to annotate: chr21:33031597-33041570
  • 2. Add data source: group (custom tracks), track (SYDH…) [click

add]

  • 3. Now choose which annotations you want to add by [add]ing more

tracks to the list – ex:

  • 1. Find the genes that overlap with your regions: group (Genes and

Gene Prediction), track (GENCODE V19), view (Genes), subtrack (Basic) [add]

  • 2. Find the SNPs that overlap with your regions: group (Variation),

track (Common SNPs) [add] Choose which fields to include in your output: Output options -> Choose fields [Done] -> [get output]

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Exercise 4

Annotate your VCF with the Variant Annotation Integrator

  • 1. Go to the Variant Annotation Integrator
  • Tools -> V.A.I.
  • 2. Select Variants:
  • Variants: “VCF Ex. 1…”
  • 3. Now choose which annotations you want to add:
  • To determine which gene regions your variants fall into, select a

gene track (Select Genes = “Basic Gene Annotation Set… GENCODE”)

  • Add regulatory annotations: Under “Select Regulatory

Annotations” click the “+” button to choose which TFs to include (or select none to include all binding sites)

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Bonus Material!

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Where to search

genome.ucsc.edu/cgi-bin/hgGateway

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Where to search

genome.ucsc.edu/cgi-bin/hgGateway

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Where to search: Main Browser

genome.ucsc.edu/cgi-bin/hgTracks

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Public Hubs

My Data Track Hubs

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Where to search

genome.ucsc.edu/cgi-bin/hgHubConnect

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Track search

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Track search

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Track search