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mkdir BDIB_IGV_export
cp -i NC_012967.1.gbk.gff BDIB_IGV_export  # copy the new file you just converted to the export directory
cp -i $SCRATCH/BDIB_bowtie2_mapping/NC_012967.1.fasta BDIB_IGV_export
cp -i $SCRATCH/BDIB_samtools_tutorial/NC_012967.1.fasta.fai BDIB_IGV_export
cp -i $SCRATCH/BDIB_samtools_tutorial/SRR030257.vcf BDIB_IGV_export
cp -i $SCRATCH/BDIB_samtools_tutorial/SRR030257.sorted.bam BDIB_IGV_export/bowtie2.sorted.bam
cp -i $SCRATCH/BDIB_samtools_tutorial/SRR030257.sorted.bam.bai BDIB_IGV_export/bowtiebowtie2.sorted.bam.bai
tar -czvf BDIB_IGV_export.tar.gz BDIB_IGV_export

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pwd

scp -r <username>@ls5.tacc.utexas.edu:<full_path_to_IGV>/BDIB_IGV_export.tar.gz .
# enter your password 
tar -xvzf BDIB_IGV_export.tar.gz

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1. Expand
   title Locally on the classroom machines booted in Mac OSX
   Click here to download and install the mac application version. Save it to your desktop, then extract the zip file and launch the application.

2. Expand
   title Locally on the classroom machines booted in Linux
   This downloads the IGV executable and tells the command line to launch it (via the java command). Code Block wget http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.32.zip unzip IGV_2.3.32.zip cd IGV_2.3.32 java -Xmx2g -jar igv.jar

3. Expand
   title In a Web browser
   Navigate a web browser to this page:http://www.broadinstitute.org/software/igv/download. You will need to register your email address to use this option, but in years of registration I have never noticed any emails from them. 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. Warning title Mac warning This will not work on recent Mac OS updates without severely modifying security permissions as administrator (which you can not do on a classroom computer). Recommended to use Mac directions above during the class.

4. Expand
   title Locally on a Mac or Windows computer
   Click here to download version 2.3.53 of IGV or visit https://www.broadinstitute.org/software/igv/download to download the latest binary version. 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. Warning title Mac warning This will not work on recent Mac OS updates without severely modifying security permissions as administrator. Recommended to use Mac directions above.

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We're really interested in places in the genome where we think there are mutations. In the Variant calling tutorial we identified such locations but lacked a good way to visualize them. This is your opportunity to visualize them. We have already transferred the SRR030257.vcf file back to your local computer, but before we can visualize them, we need to (guess what?) index it.

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It will look like nothing has happened aside from the appearance of "Done" in the messages box, but you can now close the "Run" window and choose File > Load from File. If you navigate to your IGV directory, you will now see a brand new SRR030257.vcf.idx file. You can now load the SRR030257.vcf file, and it will show up as a new track near the top of your window.

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• Zoom in using the slider in the upper right. Do this until you see mapped reads and finally individual bases appear.
• Navigate by clicking and dragging in the window. This is how you move left and right along the genome.
• Navigate more quickly. Use page-up page-down, home, end.
• Jump to the next point of interest. Click on a track name on the left side of the window (Ex: bowtieSRR030257.vcf), to select it. You can then use control-f and control-b to jump forward and backward within that list of features. Try this on the variant calls track.
• Jump right to a gene. (If you have gene features loaded.) Type its name into the search box. Try "topA".
• Load multiple BAM alignments or VCF files at once. Try this to compare a few different regions between the bowtie and BWA results.
• Change the appearance of genes. Right click on the gene track and try "expanded". Experiment with the other options.
• Change the appearance of reads. Right click on a BAM track and choose "show all bases" and "expanded". Experiment with the other options.

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1. Download and install the Integrative Genome Viewer from the Broad Institute. 
2. Select "Human hg19" as the reference genome from the top left drop down (you may need to select "more" to have hg19 as an option)
3. Get some data: File > Load from Server… > 1000 genomes > Alignments > ACB > exome > HG01880
4. Navigate to the rightmost exons of the GABBR1 gene.
5. Zoom in until you find some SNPs. (Hint look just to the left of the 2nd exon).
6. What type of library is this? (Hint: zoom out)
7. If you knew this was a cancer patient, consider how strongly you would think this may be a potentially causative mutation.
8. Imagine it was actually in the exon rather than just into the intron... would that make you consider it more?
9. Load and look at the SNP track: File > Load from server > Annotations > Variants and Repeats > dbSNP 1.3.7
10. The track may load with the Refseq genes, making it useful to resize that window to view both the gene and the dbSNP information simultaneously.
11. Consider if this makes you think it more likely or less likely that this is a causative mutation.

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Optional Tutorial Exercises ...

samtools faidx NC_012967.1.fasta
samtools view -b -S -o bowtie/SRR030257.bam bowtie/SRR030257.sam
samtools sort bowtie/SRR030257.bam bowtie/SRR030257.sorted
samtools index bowtie/SRR030257.sorted.bam

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