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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
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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
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UCSC Genome Browser http://genome.ucsc.edu
Local: http://membrane.wi.mit.edu/
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Global View
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Genome Viewer
Tracks (group of data)
Navigation
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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
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Track description
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Item description
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configure
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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
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5’UTR 3’UTR Coding exon
Intron
Commonly used gene models GENCODE, Ensembl, UCSC, Refseq
View genes/exons only
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multi-region
Browser Tracks
click links for detail information
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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.
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ENCODE super track settings
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ENCODE track setting
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ENCODE: genome.ucsc.edu/ENCODE/
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ENCODE: search tracks
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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?
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Add custom track
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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
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Bed: regions Enriched Chip-seq signal for TF binding
Wig(gle): continues signal Chip-seq signal
BAM: alignment of reads RNA-seq alignment
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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
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Convert to other genome/build
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Save to file
Convert to other genome/build LiftOver: multiple regions
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blat: align sequences
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view alignment in browser
Track Data Hubs
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Share/save session
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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
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