# NSCI 580A3 fall 2017

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NSCI 580A3

Instructors
Tai Montgomery
Erin Nishimura

wiki2016nsci580a3assignment1

# Assignment 1

Due date: 11/28 by 10 am

WHEN ACCESSING THE SERVER, USE GNU SCREEN TO ENSURE THAT JOBS CONTINUE TO RUN IF YOU LOSE YOUR CONNECTION.

screen - enter gnu screen

ctrl+a+d - detach window

screen -r - resume a detached window

Using the tools demonstrated in class, identify genes that are differentially regulated in alg-1 loss of function C. elegans relative to wild type C. elegans.

Alternatively, you can analyze a dataset of your choosing as long as the data is relevant to your research and contains biological replicates.

There are a total of six paired-end libraries (12 total fastq files): three biological replicates from each of the two strains. The fastq files are located in your home directory on the server rna.biology.colostate.edu:
/home/lastname/alg1

The file names are:

• wt_1_1.fastq.gz
• wt_1_2.fastq.gz
• wt_2_1.fastq.gz
• wt_2_2.fastq.gz
• wt_3_1.fastq.gz
• wt_3_2.fastq.gz
• alg1_1_1.fastq.gz
• alg1_1_2.fastq.gz
• alg1_2_1.fastq.gz
• alg1_2_2.fastq.gz
• alg1_3_1.fastq.gz
• alg1_3_2.fastq.gz

The C. elegans genome sequence and annotations are also in the alg1 folder.

For full credit, your completed assignment must include the following:

Table 1: a) the proportions of reads passing quality filtering from each of the twelve libraries and b) the proportions of alignable reads from each of the twelve libraries.

Table 2: A file containing the lines of the gene_exp.diff file generated by cuffdiff for all genes differentially regulated by >2 fold and with a q value of <0.05. Lines should be sorted by change in gene expression.

Figure 1: A volcano plot comparing wild type and alg-1 mutants - must include a figure legend.

Summary of findings: a brief, no more than one paragraph summary of your findings.