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Mapping III: Visualization
Now let's visualize the alignment files!
Download IGV from here in your local computer, if you don't have it already. Here you can find some documentation in case you need it.
Download the four alignments (DNA-bwa, DNA-bowtie, RNA-tophat and RNA-star)you created together with their indexes (*bai).
Make sure hg19 is loaded.
In the viewer go to File -> Load from file and choose the BAM files.
As first sight you can't really see the alignments unless you zoom in quite a lot. To overcome this, let's generate a coverage track. Go to Tools -> Run igvtools, select count.
Then select one of the alignments and click Run. This will create a tdf file, a pre-processed
file for faster display. Load the tdf once you have it.
Create the tdf for the other alignments and load them.
Q. In which chromosomes you have data?
Zoom in to see the alignments. Select the tdf tracks, right-click, select Set Data Range and set the maximum to 80. This to have the same scale.
Q. How does the coverage pattern look like? Can you find regions that are not expressed but are targeted in the DNA data?
By right clicking in the alignment window you will find different options. Try the following and understand what the different coloring means:
- Color alignment by:
- insert size
- read strand
- first-of-pair strand
Inspect also:
- View as pairs
Q. Are you able to identify any SNPs? How are deletions/insertions depicted?
You can also right-click on the RefSeq Genes track, and select Expanded. This will
let you see the different splice variants.
Q. Can you find splice variants that are not targeted? Are microRNAs or other non-coding RNAs targeted/expressed?
Previous: Mapping II: Aligners
Created by Marcela Dávila