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Exercise 12

Small RNA data analysis (part 3): data visualization

1. Open IGV and select the C. elegans genome WS220 from the dropdown men (top left, select more to see additional genomes available).

2. Reformat the wild type and prg-1 mutant bam files to tdf format using igv tools:

Tools > Run igvtools
Under Command, select Count and Run
Under Input file, select the sorted.bam file
Close igv tools when complete

3. Load the two tdf formatted files into IGV:

File > Load from File
Select the tdf file that contains sequencing data created in step 3 above
Right click on the plot to modify the parameters - change track height, track color, and data range. 

4. Enter the chromosome coordinates for each miRNA, siRNA, and piRNA gene and examine how the small RNA reads differ between wild type and prg-1.

5. Go to the wormbase website and search for prg-1. What family of genes does prg-1 belong to and what is its function? Are the results consistent with the function of prg-1?

Submit your answer to the following question on Canvas:

What were the six major steps in our analysis of the small RNA data in exercises 10-12, starting with '1. Quality control using FastQC'?

assignments/ex12.txt · Last modified: 2017/10/27 14:36 by dokuroot