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wiki2016assignment1 [2016/10/31 16:17] (current)
tai created
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 +====== Assignment 1 ======
 +
 +**Due date:​** ​ 11/18 by 10 am
 +
 +Using the tools demonstrated in class, identify genes that are differentially regulated in //alg-5// loss of function //C. elegans// relative to wild type //C. elegans//​.\\
 +
 +There are a total of six libraries: three biological replicates from each of the two strains. The ''​fastq''​ files are located in the ''​RNA-seq''​ directory: ''/​Users/​GraduateStudent/​Documents/​RNA-seq''​.\\
 +
 +The file names are: ''​wt_1.fastq'';​ ''​wt_2.fastq'';​ ''​wt_3.fastq'';​ ''​alg-5_1.fastq'';​ ''​alg-5_2.fastq'';​ and ''​alg-5_3.fastq''​.\\
 +
 +The //C. elegans// genome sequence and annotations are in ''/​Users/​GraduateStudent/​Documents/​RNA-seq/​C_elegans_Genome''​.\\
 +\\
 +
 +**For full credit, your completed assignment must include the following:​**
 +  - The proportions of alignable reads from each of the six libraries.
 +  - 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.
 +  - An MA plot comparing wild type and //alg-5// mutants.
 +
  
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