Download IGV Handout file

Integrative Genomics Viewer
The Integrative Genomics Viewer is a visualization tool for exploring
and analyzing large genome datasets. It is a lightweight genomic data
viewer on which you can work with prebuilt genomes or load any
genome that you want. It may be used for viewing a variety of data
such as expression data, NGS alignments, microarray, epigenomics,
RNA-Seq, genomic annotations etc. IGV has a friendly user interface.
You may run it locally on your desktop or launch it from the Broad
Institute website. You must register for launching or down loading. It is
a Java application and you will need to install Java 6 or later on your
desktop.
I.
Launch or download IGV
1. Go to this web page:
http://www.broadinstitute.org/software/igv/download.
2. The first time you sign on, you will need to register to
download IGV.
3. Click on the first launch icon (Launch with 750MB); 750MB is
the smallest memory available and is sufficient for most
applications.
4. Save it on the desktop as an IGV icon. When you need to
start IGV, simply click on this icon.
Notes: Alternatively, you may download IGV zip file; unzip it and install
on your desktop. However, if you want to start IGV from command line
(UNIX) you will need the binary distribution. You may also need SAM
Tools and IGV Tools. These are described later
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II. IGV User Interface
A. Main Window
1 Tool Bar
2 Chr ideogram
displayed in red
3 Ruler
4 Tracks
5 Genes
6 Track names
7 Attributes
Access various functions
Indicates the area of the chromosome
currently displayed
The tick marks show chromosome
locations
Data is displayed in tracks. Each track
represents a sample or an experiment
Displays features such as genes
Each track is assigned a name
Each attribute has a name. The values
are displayed as colored blocks
B. Tool Bar (Source: IGV User Guide)
Genome drop-down box
Loads a genome
Chromosome drop-down
box
Zooms to a chromosome
Search box
Whole genome view
Displays the chromosome location being
shown. To scroll to a different location,
enter the gene name, locus, or track
name and click Go. ..
Zooms to whole genome view
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Moves backward and forward through
views of the genome like the back and
forward buttons in a web browser.
Refresh
Define a region
Refreshes the display.
Defines a region of interest on the
chromosome
Reduces the row height on all tracks to
fit all data for the region in view into the
window; will also expand tracks (to their
maximum preferred size) to fill the view,
if needed.
Toggles the pop-up information
windows in IGV on or off.
Zoom slider
III.
Zooms in and out on a chromosome.
Sometimes referred to as the "railroad
track."
IGV Exercises
Following short exercises will demonstrate the various
functionalities of IGV. Create a directory called igvdata and
download following file for these exercises (instructions to
download will be provided separately):
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dnai1.reads.sam
Ex. 1. Load a genome and define region of interest (7-9)
a. Click on genome box down arrow; click on More: a
number of prebuilt genomes will be displayed.
b. Select A. thaliana (TAIR9) to load the genome.
c. Click on Chr 1.
d. Select an area on the chromosome; this will be the region
of interest and will be displayed as a red block on the
chromosome ideogram.
e. Use the Zoom Slider (upper right) to zoom in till you see
the gene sequence (bases) at the bottom of the screen.
Ex. 2. Load a prebuilt genome; search for a gene, view
gene sequence, translate to amino acid sequence, and
copy sequence to the desktop. (10-15)
f. Click on genome box down arrow; a number of prebuilt
genomes will be displayed.
g. Select Human HG19 to load the genome.
h. Click on Chr 9. Chromosome ideogram is displayed under
the Tool Bar; gene features are displayed at the bottom.
i. Select an area on the chromosome; this will be the region
of interest and will be displayed as a red block on the
chromosome ideogram. Note the number of base pair
displayed in the current window.
j. Zoom in till you see the gene sequence (bases) at the
bottom of the screen.
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k. Navigate by clicking and dragging the main portion of the
window in order to move left and right on the genome.
l. Search for a bladder cancer gene, DAPK1. Type DAPK1 in
the search box on the top and click Go.
m. DAPK1 gene is displayed at the bottom. Zoom in till you
see the bases.
n. Right click on the gene sequence and select Translate to
see the amino acid sequence.
o. Right click on the chromosome and copy the sequence to
the clipboard. Save it in igvdata directory.
Ex. 3 Use IGV Tools to sort a file, create an index file,
and create a .tdf file.
i. Sort an input file – dnai1.reads.sam
a. On the Menu bar click Tools > igv tools > sort.
b. Click Browse and point to the input file name
(dnai1.reads.sam) in the igvdata directory.
c. Click run;
dnai1.reads.sorted.sam will be created and saved in
the igvdata directory.
ii. Create an index file on dnai1.reads.sorted.sam
a. On the Menu bar click Tools > igv tools > index.
b. Click Browse and point to the input file name
(dnai1.reads.sorted.sam) in the igvdata directory.
c. Click run;
dnai1.reads.sorted.sam.sai will be created and saved in
the igvdata directory.
iii. Create a binary tiled data file (.tdf) on
dnai1.reads.sorted.sam
a. On the Menu bar click Tools > igv tools > to TDF
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b. Click Browse and point to the input file name
(dnai1.reads.sorted.sam) in the igvdata directory.
c. Click run;
dnai1.reads.sorted.sam.tdf will be created and saved in
the igvdata directory.
Ex. 4 Use SAMTOOLS to convert a SAM file to a BAM file; sort
the BAM file; create an index file
BAM is the binary equivalent of the SAM (Sequence Alignment Map
format). These formats are used for conveying alignment mapping
information. BAM files are frequently used for various kinds of
analyses.
SAMTOOLS is an open source program, available at samtools website
or sourceforge.net. It needs to be downloaded, unzipped and installed.
Commands are given on the command line in the UNIX environment. If
you happen to be using Windows computer, you may buy a KNOPPIX
(LINUX) DVD or download Linux on a cd and make it executable. This
will allow you to boot your computer from the DVD/CD and work in the
UNIX environment.
i. Start SAMTOOLS and make it executable with make
command
a. Point to SAMTOOLS-0.1.19 in the igvdata directory.
b. Right click > open in terminal
c. make
j. Convert a SAM file to a BAM file
a. ./samtools view –b –S dnai1.reads.sam >
dnai1_reads.bam
(Give the full path name of the input file such as:
/media/sdb1/igvdata/ dnai1.reads.sam).
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Note: You may convert SAM to BAM in Galaxy if you are
familiar with it.
ii. Sort a BAM file
In order to create an index BAM file, it needs to be
sorted first.
./samtools sort –m 1000000000 dnai1_reads.bam
dnai1_reads_sorted.bam
Note: Modifier –m indicates the amount of memory that can
be used
iii. Create an index file on dnai1_reads.sorted.bam
a. ./samtools index dnai1_reads_sorted.bam
b. dnai1_reads_sorted.sam.sai will be created and saved
in the same directory as the input file.
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