.Robert Kuhn

UC Santa Cruz.

Variant Prediction Workshop.

Heraklion, Greece

November 2, 201611:45 am

UCSC Genome Browser

@GenomeBrowser

Genomes

hg38 altsSessions, incl. Public Sessions

Custom Tracks

BAM

VCF

Multi-region

Exon-only

hg38 alt regions

Upload list of genes

http:// genome-euro.ucsc.edu

http:// bit.ly/vep2016

>>>>>

Genome Browser:A tool for inquiry-driven discovery

Data pipeline

slide modified from:

Tim Hubbard, King’s College, London

100K genomes (rare disease or cancer)

Variant Annotation Integrator

BAM track

Wiggle track

BAM track

bamToBedGraphbedGraphToBigWig

bedGraph track

Data pipeline

YouTube training channel: bit.ly/ucscVideos

On-site workshops (training link on main page):http:// genome-euro.ucsc.edu/training

Overcoming large-file upload limits

Remote, binary, indexed filetypes

file

to UCSC

Typical Custom Track:File is uploaded to our server

(large)

bigBed, bigwig, BAM or VCF Custom Track: File lives on your server, but is indexed. Only local display information is uploaded

fileto UCSC

(small)

file

ftp, http, https

to UCSC

URL Custom Track:File lives on your server, but is fully uploaded when invoked

(large)

ftp, http, httpsindexed

VariationWatson: 2.06 million SNPsVenter: 3.32 million SNPs

1.19 million in common

In 20 kb myoglobin region on chr22, Watson and Venter share 20 SNPs. Watson has 9 unique SNPs, Venter 6.

VariationWatson: 2.06 million SNPsVenter: 3.32 million SNPs

1.19 million in common

VariationWatson: 2.06 million SNPsVenter: 3.32 million SNPs

all human SNPs

VariationWatson: 2.06 million SNPsVenter: 3.32 million SNPs

one chimp

Exon-only

RNA-seq data from CSHL, ENCODE project

user: example

session: hg19_exonsExpression3

Defined regions

Start with genes: FGF1, FGFR{1,2,3,4}

Get their coords

Load into URL; display

Alternate haplotypes

Map ends of alt with BLAT

Swap alt into place

Live demo:

http:// genome.ucsc.edu