Page Comparison

...

mkdir BDIBGVA_IGV_export
cp -i NC_012967.1.gbk.gff GVA_IGV_export  # copy the new file you just converted to the export directory
cp -i $SCRATCH/GVA_bowtie2_mapping/NC_012967.1.fasta GVA_IGV_export
cp -i $SCRATCH/GVA_samtools_tutorial/NC_012967.1.fasta.fai GVA_IGV_export
cp -i $SCRATCH/GVA_samtools_tutorial/SRR030257.vcf GVA_IGV_export
cp -i $SCRATCH/GVA_samtools_tutorial/SRR030257.sorted.bam GVA_IGV_export/bowtie2.sorted.bam
cp -i $SCRATCH/GVA_samtools_tutorial/SRR030257.sorted.bam.bai GVA_IGV_export/bowtie2.sorted.bam.bai
tar -czvf GVA_IGV_export.tar.gz GVA_IGV_export

...

There are multiple ways to launch IGV on a local computer, in decreasing order of recommendation due to recent mac OS updates and easy of use:

1. Expand
   title Locally on the classroom machines booted in Mac OSXyour laptop with application version
   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 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 is a bit much to do for this class if you dont don't continue to use it).

3. Expand
   title Locally Install the full version on a Mac or Windows computer
   Click here to download version 2.5.2 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.

...

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.

...

• Why are some reads different colors? Hint: Try changing the display options to show read pairs and editing some of the distance constraints.

• Interested in determining the probability that a read is not where it should be? What is a typical mapping quality (MQ) for a read? Convert this to the probability that it is mismapped.

  Expand
  title Remember Click here for the formula for a Phred quality score?.
  The estimated probability that a read is mapped incorrectly is 10^(-MQ/10). Where MQ is the mapping quality.

• Can you find a variant where the sequenced sample differs from the reference? This would be like looking for a needle in a haystack if not for the use of variant callers and the control-f and control-b options to zoom right to areas where there are discrepancies between reads and the reference genome that might indicate there were mutations in the sequenced E. coli.

  Expand
  title Some interesting example coordinates
  Expand title Coordinate 161,041. What gene is this in and what is the effect on the protein sequence? Gene is pcnB, mutation is a snp Expand title Coordinate 3,248,957. What gene is this in and what is the effect on the protein sequence? Gene is infB, mutation is a snp Expand title Coordinate 3,894,997. What type of mutation is this? Deletion of the rbsD gene Expand title Check out the rbsA gene region? What's going on here? There was a large deletion. Can you figure out the exact coordinates of the endpoints? Navigate to coordinate 3,289,962. Compare the results for different alignment programs and settings. Can you explain what's going on here? Expand Answer Answer There is a 16 base deletion in the gltB gene reading frame. What is going on in the pykF gene region? You might see red read pairs. What does that mean? Can you guess what type of mutation occurred here? Expand Answer Answer The read pairs are discordantly mapped. There was an insertion of a new copy of a mobile genetic element (an IS150 element) that exists at other locations in the reference sequence. See if you can find more interesting locations. There are ~40 mutations total in this sample MOST of which are false positives.

...