NOTE: All instructions in this document should be performed on your laptop, not on the RStudio Server AMI.
We'll first create a directory called “igv” in your home directory. You can determine your home directory by issuing the following command in a Terminal window on Linux or Mac:
On Windows, open a command window by clicking Start, then Run, then
cmd and pressing Enter. In the window, type
So go to the indicated directory, and then issue the command
That will create an
igv directory in your home directory.
Copy the file hg19_alias.tab to this directory. This is a simple tab-delimited file that maps between the sequence names used by the alignment, and the sequence names known to IGV.
Install Java if you haven't already. Go to https://www.java.com/en/ and click on Free Java Download. Download and install.
Download IGV from https://www.broadinstitute.org/igv/download. There are several ways to do this, the easiest is to click on one of the Java Web Start links. Make sure you have more memory available than what is listed below the Launch button. You may need to change the security settings on your computer to allow IGV to launch.
With IGV running, let's change the default genome. It's currently
set to Human hg18, so click on the dropdown in the upper left
that says “Human hg18”. Click on “More…” and then in the
Filter box, start typing
Human hg19 will then show
up in the box and you can double-click on it. We're now using
Human hg19 as our default genome.
You can now open bam files in IGV. Here are the URLs of
BAM files for this class. You can open them by clicking on
File menu, then clicking on
Load From URL....
You can paste one of these URLs into the box and click OK:
http://s3-us-west-2.amazonaws.com/oct2014bamfiles/SRR1039508_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/SRR1039509_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/SRR1039512_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/SRR1039513_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/SRR1039516_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/SRR1039517_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/SRR1039520_sorted.bam http://s3-us-west-2.amazonaws.com/oct2014bamfiles/SRR1039521_sorted.bam
You may see a warning that the bam file does not contain any sequence names which match the current genome. You can ignore this (click OK).
Go. Adjust the zoom until reads come in to view, and interpret the result.