Due date: December 11, 2016, 10:00am
Submit your assignment on canvas
Start an RNA-seq analysis project using automation
Create a copy of the script file from the yeast demo
HINT: The script will take about 40 minutes to run. You'll need to switch the following sbatch conditions:
Turn in the text of the summary outputs from featureCounts. Typically these are .txt.summary files. This can only be submitted as a .txt file or copied and pasted into canvas as .txt documentation. No word files, No fancy text.
Explore the merged .bw files on UCSC Genome browser (link below). Alternatively, you can download all or any subset of your own .bam or .bw files and explore them on IGV.
The manuscript Gomez-Orte et al., 2018 contains a supplemental dataset that lists all the genes that are up-regulated in E.coli versus B.subtilis independent of temperature. Use the genes on this list to scan through the genome browser. I'm attaching the dataset here: Supplemental Dataset 13
Assignment: Make a figure out of a browser shot (IGV or UCSC, you choose) of one of the genes on the list (you choose). Include a figure legend. You can make the figure any way you like… powerpoint, illustrator, anything. Upload a .pdf of your figure to canvas.
Hint: If you would like to see an example of some genome browser shots I recently made into figures, check out Figure 4B of this paper: Dineen and Osborne Nishimura et al., 2018