UCSC Genome Browser
ASHG 2014 Workshop
We will be using human assembly hg19. Some steps may seem a bit cryptic or truncated.
That is by design, so you will think about things as you go….
In this document, if you see something in square brackets, e.g, [submit], look for a button
with that label:.

1. Load Custom Tracks.
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On genome.ucsc.edu, follow “Genome Browser” link to the Browser Gateway.
Click link: “Click here to reset.”
Navigate to hg19 [submit]. Then: [hide all]In the Genes and Gene Prediction bluebar track group, turn on UCSC Genes to “pack”[refresh]
Below the Browser graphic, find button: [add custom tracks]
or: [manage custom tracks] then [add custom tracks]
In a separate window/tab, go to bit.ly/ucscASHG2014 and click into ctExamples.txt.
Copy either the url for this page or its contents into the upper box on the Custom
Track imput page, “Paste URLs or data” [Submit]
On the new page, click into top link in the “Pos” column, labeled “chr6”
Observe the relationship between the items in the Browser graphic and the data you
copied from the other page.
These are a few of the 14 data types available.

2. Visualize a BAM-file Custom Track.
The Genome Browser display of BAM files shows coverage, mappings of individual
sequence reads, base-pair mismatches and quality scores.
 To load a BAM file, it must be indexed (create a .bai file) and placed on a server
visible to the Web (and the Browser) via http: protocol.
 We have placed a file on a server for you to load (the filename is in the bigDataUrl
portion of URL a few steps below).
 Below the Browser graphic, click [add custom tracks]
or: [manage custom tracks] then [add custom tracks]
At the top of the page, select:October 20 2014UCSC Genome Browser Workshop

ASHG,2014assembly: hg18
In the upload (upper) box, type or copy (all on one line):
track name=chr21_export type=bam bigDataUrl=http://genometest.cse.ucsc.edu/ABRF2010/chr21.bam visibility=pack[submit]

New page. [go to genome browser]
Back at the Browser, navigate to this interesting location:
chr21:37,366,714-37,366,825

Turn on the UCSC Genes and SNPs (130) tracks (This older version works because
we are on hg18).
 Zoom out 10x a couple of times. Observe.
To see this result all at once, you can load a session: Under Restore Settings, type (orclick “BAM result” on workshop webpage):
user: example
session name: hg18_bamSnps [submit]At the top of the page, where it says, “Updated Session,” click “Browser.”3a. Table Browser Join: Load a list of genes into the Table Browser andextract info from joined tables.
In a separate window/tab, go to bit.ly/ucscASHG2014
Click to genelist and copy contents.
In genome.ucsc.edu, use the “Tools…” pulldown and choose “Table Browser”
In Table Browser, choose
group: Genes and Gene Predictions
table: knownGene
track: UCSC Genes
region: genome
identifiers: [paste list]
paste list into box [submit]
output format: selected fields from primary and related tables [get output]

On the new page, select from the knownGene table:
chromtxStarttxEnd
note: knownGene.name is an internal UCSC identifier and NOT the common
name for the gene.

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From the kgXref table, select:geneSymbol (THIS is the name of the gene)description
 [get output]

3b. Repeat this, getting only one isoform per gene.
Back at the Table Browser, follow the same process, except choose:
table: knownCanonical

4. Table Browser Intersection / Subtraction. We will create a Custom
Track of uncommon SNPs by subtracting Common SNPs from All SNPs.
First, check out how big the All SNPs (dbSNP 138) table is:
At the bottom of the Genome Browser graphic page, find the Variation bluebar groupand “All SNPs (138)” link above its pulldown track controls. Click the link.
 On the new page, click “View table schema.” Note the Row Count: 65.5 M! … andnotice all the other data available for each SNP.
 We’ll work with a small subset of SNPs, because it is very slow to do an intersection
with such a large table, especially when we are all doing it at once!
LOAD A SESSION
 We have created a pair of tracks that contain only a few thousand SNPs from the All
SNPs (138) and Common SNPs (138) tables – covering only 250 kb of chr4, about
0.01% of the genome.
 Starting from the main Browser graphic page, go the pulldown, “My Data” and select“Sessions.” Under Restore Settings, type:user: example
session name: hg19_ashg2014_SNPs [submit]At the top of the page, where it says, “Updated Session,” click “Browser.”
Choose a small portion of this 250 kb to zoom and see the difference between thesetwo tracks.

TABLE BROWSER INTERSECTION
 We will be subtracting Common SNPs from All SNPs, using our small set of a few
thousand, and saving the result in a new Custom Track.
 Go to the Table Browser (via “Tools…” pulldown) Choose:group: Custom Tracks
track: 4q21.1 all SNPs (primary table)table: (accept default)
region: genome
intersection: [create]October 20 2014
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ASHG,2014

On new page:group: Custom Tracks
track: 4q21.1 common (secondary table)table: (accept default)
select the second button:
All 4q21.1 all SNPs records that have no overlap with 4q21.1 common[submit]Back at Table Browser main page:
output format: custom track [get output]

On the new page, give the track a name (“uncommon” ?) and long label.
visibility: dense [get custom track in genome browser]If you are lost, you can see the result here (or click “SNP result” on the workshopwebpage):
user: example
session name: hg19_ashg2014_snpResult
 zoom out a few times

5. Make a filter in the Table Browser to obtain only the data that exceed
some value.
We will make a track that contains only the strongest vertebrate conservation signal atthe FGFR1 locus. We will confine ourselves to a small region to avoid slow
processing times.
 Start by loading a session that looks at the 3’ end of the FGFR1 gene, with theConservation track turned on (or click “Filter input” on the workshop webpage):
user: example
session name: hg19_FGFR1cons

Note that the maximum value displayed for the PhyloP Conservation track is 4.88 (leftmargin), and that some of the peaks have a pink “hat” on top, indicating that the value
extends off the scale. A reasonable cutoff to get the tallest peaks is 4.0.
 Click into one of the peaks to go to the details page and then note the table name at the
top: phyloP100wayAll .
 Go to the Table Browser (“Tools …”) and set it to that table:group: Comparative Genomics
track: Conservationtable: phyloP100way (the default)
position: (button) (accept the default coordinates which match the region on
Browser graphic).
PLEASE DO NOT LEAVE “genome” SELECTED !
filter: [create]October 20 2014

UCSC Genome Browser Workshop

On the new page:
data value is: > 4.0

ASHG,2014[submit]Back at Table Browser page:
output format: custom track [get output]

Make up a name for short and long labels (“topOfPeaks” ?). [get custom track ingenome browser]

ADJUST SCALES OF CUSTOM TRACK AND PHYLOP TRACK TO MATCH
 To make the two tracks look like they belong together and have the same verticalscale, we will configure the scales and windowing to match each other. (Windowing:
Because the display must combine the data for more than one nucleotide per pixel, achoice must be made about how to display the data. The default “windowing” on thephyloP track is “mean,” which smoothes out the values -- especially any negativevalues, as you will see).
 Right-click the phyloP track. Choose “Configure 100 Vert. Cons”
Vertical viewing range: min: -2
max -4 (to match cutoff we used in filter)
Windowing function: maximum

Right-click and configure your new Custom Track.
Track height: 50 (to match phyloP default)
Vertical viewing range: min: 4max: 10 (to match phyloP range of 6)
Data view scaling: use vertical viewing range setting
Windowing function: maximumTo see what this display should look like at this point, load (or click “Filter result” onthe workshop webpage):
user: example
session name: hg19_FGFR1consResults

6. Use the Variant Annotation Integrator (VAI) to classify SNP variants.
The VAI tool will take files of variants in VCF or pgSnp format and return
information about the biochemical effects of the variants.
 Start by loading a session that reloads the Custom Tracks in #1 above (or click“Custom Track result” on the workshop webpage):
user: example
session name: hg19_ctExamplesResultOne of the Custom Tracks, My SNPs -- Personal Genome SNP format, is in pgSnp
format, and is suitable for the VAI (the other supported format is VCF).

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If you open the VAI in the next step in a separate tab or window, you will be able tocompare the results from the VAI to the Browser graphic.
 In the “Tools…” pulldown, select “Variant Annotation Integrator”
 In the Select Variants section:variants: My SNPs – Personal Genome SNP format (should be the default)
In the Select Genes section, choose: Basic Gene Annotation Set from GENCODE
Version 19.
 Notice the large number of annotation options, including Regulatory Annotations.
Select any option (or accept default), then near the bottom, under Configure Output,
output format: Variant Effect Predictor (HTML) [get results]
Note the types of information provided: Gene; Consequence (misssense, frameshift,splice_donor_variant, {up,down}stream_gene_variant (and distance)); Co-locatedVariation (+dbSnp rs#, if available); SIFT, PolyPhen scores, etc.

Coming in VAI 2.0: sorting by variant type.