Due date: December 7, 10am
NOTE This is listed on Canvas as “Exercise 2”
Which genes are expressed in a specific tissue type? In this Assignment you will analyze an RNA-seq project whose aim is to determine genes that are enriched in the intestines of C. elegans worms compared to the animal as a whole.
$ cd $ cp -R /home/erin/03_htseq_homework/ .
Align and tabulate the sequencing files for this dataset. To do this, you may need to…
RNAseq_analyzer.shby amending the “MODIFY THIS SECTION”. Use the C.elegans bowtie2 indices and .gtf file from Assignment 1.
To illustrate your success, please turn in the following two figures on a standard, letter-sized .pdf document…
# of mapped readsfor each sample and the
% overall read mapping ratefor each sample. Include a table legend.
In this exercise, you will use DESeq2 to identify differentially expressed genes.
/home/erin/05_deseq_homeworkto your own home directory.
To illustrate your work…
Find a paper in your field that has performed RNA-seq. Read their methods section to determine how they performed and analyzed their RNA-seq experiment.