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
The file names are:
The C. elegans genome sequence and annotations are also in the
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.