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- *If you have an
intro_to_mappingdirectory with output from the Mapping tutorial or the Variant calling tutorial, then you should use those files for this tutorial. - If you do not have any results, you can use some "canned" ones that we provide. Copy the entire contents of this directory back to your local machine:
Then skip down to #Launching IGV.Code Block $BI/ngs_course/intro_to_mapping/IGV
Prepare a GFF feature file for the reference sequence
IGV likes its reference genome files in GFF (Gene Feature Format). Unfortunately, our old friend bp_seqconvert.pl doesn't do GFF. Fortunately, it's cousin bp_genbank2gff3.pl does with this command:
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Another useful trick with either IGV or UCSC: displaying your own BLAST results: BioPerl allows for super-easy conversion from blast output to a gff file; IGV and the UCSC browser both understand GFF files. The short script Let's use the blast result we had from the earlier test for the JAG1 gene to show you how. You'll need to provide the input file - it's the ".oNNNNNN" output file from your blast job.
The resulting jag1_blast.out.gff can be moved to your local machine and opened in IGV. Load the human reference first though! |
If you have only done the mapping tutorial and NOT the variant calling tutorial
You will need to index your reference FASTA and convert your SAM output files into sorted and indexed BAM files. The "why?" behind these steps is described in the Variant calling tutorial. If you are in your
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Repeat the last three commands for each SAM output file that you want to visualize in IGV.
Copy files to your desktop
IGV is an interactive graphical viewer program. You can't run it on TACC, so we need to get the relevant files back to your desktop machine.
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Launching IGV
There are two ways; Launching IGV in your web browser or by downloading the binaries locally and running IGV from your machine.
In Browser
Navigate a web browser to this page:http://www.broadinstitute.org/software/igv/download
Go ahead and click on the "Launch with 2 GB" option. This will download a "Java Web Start" file that you can launch by locating it on your Desktop and double-clicking.
Locally on the classroom machines booted in Linux
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wget http://www.broadinstitute.org/igv/projects/downloads/IGV_2.1.22.zip unzip IGV_2.1.22.zip cd IGV_2.1.22 java -Xmx2g -jar igv.jar |
Locally on your own Mac or Windows computer
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Use this link to download IGV http://www.broadinstitute.org/igv/projects/downloads/IGV_2.1.22.zip |
After unzipping, you should be able to click on igv.bat for Windows or igv.command on MacOSX to lauch IGV. If this is not working, you might need to try the web start.
Load genome into IGV
From the main window of IGV, click on File -> Import Genome and you should be presented with the following window.
Enter the ID and Name of the Genome you are working with and select the path to your *.fasta file (the index, *.fai file needs to be in the same directory), then select the path to your *.gff file for the Gene File.
Load mapped reads into IGV
From the main window of IGV, click on File -> Load File. Choose bowtie.sorted.bam
After importing your reference genome and loading an alignment file, your screen should look similar to the following:
And you are now free to investigate different areas and their alignments in the genome.
Navigating in IGV
There are a lot of things you can do in IGV. Here are a few:
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