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Assignment 5

DSCI512: RNAseq
Due date: December 11, 2016, 10:00am
Submit your assignment on canvas

Project description

Start an RNA-seq analysis project using automation

  • Make a directory for the project on summit called PROJ07_ce_homework2
  • Make a soft link to your input folder from last time: ~/PROJ05_ce_homework/01_input
  • Make subdirectories for scripts & output

Create a copy of the script file from the yeast demo

  • Make copies of your execution and analysis scripts into your scripts folder from the place where you downloaded the scripts during class. They are probably in /scratch/summit/<eID>
  • Modify the scripts so they will work for C. elegans.
  • Run the scripts.

HINT: The script will take about 40 minutes to run. You'll need to switch the following sbatch conditions:

  • Time: Give it an hour
  • QOS: Switch from testing to normal
  • Partition: switch from shas-testing to shas

Turn in the following

1. summary output file upload

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.

2. figure of a genome browser shot

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.

C. elegans homework genome browser

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


  • Make notes of what you did for this homework in your computational notebook.
  • Turn this in with your notebook at the end of the semester.
assignments/rna2018_assignment5.txt · Last modified: 2018/12/04 13:39 by erin