ASHG
2016
Workshop:
IntroducDon
to
the
IntegraDve
Genomics
Viewer
(IGV)
Pre-‐workshop
exercise
–
IGV
User
Interface
Basics.
1.
Download
and
launch
IGV.
• See
instruc6ons
at
[Link]/workshops/ASHG2016/[Link]
2.
Select
reference
genome.
• Click
on
Human
hg18
in
the
genome
drop-‐down
menu
in
the
upper
le>
corner.
3.
Load
data
from
the
IGV
hosted
server.
• Select
File
>
Load
from
Server…
• Open
the
Tutorials
menu
and
If
this
is
the
first
6me
you
run
IGV,
hg18
may
be
the
click
on
the
UI
Basics
checkbox.
only
entry
in
the
menu.
More
about
that
later...
Make
sure
you
do
not
check
the
box
next
to
Tutorials.
That
will
select
everything
under
Tutorials,
but
we
only
want
UI
Basics
for
this
exercise.
✔
Four
tracks
are
loaded:
ENCODE
project
ChIP-‐seq
data
represen6ng
histone
modifica6ons.
Each
track
is
displayed
as
a
bar
chart
of
signal
intensi6es.
This
type
of
data
is
perfect
for
a
UI
basics
exercise
because
the
tracks
are
visually
simple
–
but
the
naviga6on
basics
are
the
same
no
maSer
what
type
of
data
you
load.
page
1
4.
Navigate
across
different
genomic
loci
and
at
different
zoom
levels,
from
whole
genome
view
and
down
to
base-‐pair
resolu6on.
4a.
Start
at
whole
genome
view:
• Select
All
from
the
chromosome
drop-‐down
menu
–OR–
Click
the
Home
buSon.
Ruler
displays
all
the
chromosomes
At
this
zoomed
out
view,
the
gene
track
displays
gene
density
4b.
Zoom
in
to
view
one
whole
chromosome:
• Select
Chr1
from
the
chromosome
drop-‐down
menu
–OR–
Click
the
1
in
the
genome
ruler.
Genome
ruler
now
has
more
details
and
a
cytoband
view
of
the
chromosome
Gene
track
starts
showing
individual
genes,
but
s6ll
too
many
to
see
page
2
4c.
Zoom
in
further:
• Click
and
drag
to
zoom
in
on
a
region
swept
out
in
the
ruler
• Double-‐click
in
the
data
track
to
zoom
in
on
a
point
of
interest.
[Alt-‐click
to
zoom
out]
Ruler
measurements
and
a
red
box
on
the
cytoband
diagram
show
where
you
are
in
the
chromosome
4d.
Move
around
within
the
chromosome:
• Jump
to
another
region
in
the
same
chromosome
(no
change
in
zoom
level):
Click
anywhere
in
the
cytoband
diagram.
• Scroll
across
genome
coordinates:
Click
anywhere
in
the
data
panel
and
drag
le>
&
right.
4e.
Navigate
to
specific
locus
or
gene
on
any
chromosome
• Type
into
the
search
box
in
the
IGV
toolbar
and
click
Go:
either
a
locus
in
genomic
coordinates
(e.g.
chr1:144,874-‐969,268)
or
a
gene
name
(e.g.
NRAS)
page
3
4f.
Zoom
in
to
base-‐pair
resoluDon:
• Keep
zooming
in
as
before,
or
click
on
one
of
the
rightmost
6cks
on
the
“railroad
track”
zoom
widget
in
the
upper
right
corner.
Reference
sequence
5. OpDons
for
viewing
the
reference
sequence
track
• Click
anywhere
on
the
sequence
to
show/hide
a
3-‐frame
transla6on
• By
default,
the
sequence
for
the
forward
strand
is
shown.
Click
on
the
arrow
to
reverse
the
strand.
6.
OpDons
for
viewing
the
gene
track
and
other
annotaDon
tracks
IGV
uses
a
UCSD
style
gene
representa6on:
Exons
5’
UTR
Intron
3’
UTR
Features
are
drawn
in
a
single
line,
by
default
• Expand
the
track
using
the
right-‐click
popup
menu
Use
Squished
for
an
even
more
compact
view
page
4
