DM Notes 3.8.16

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Presentation on Tuesday of next week.

Today- plan making:

What have we done so far?

  • file that has organism, contig, GO IDs associated
  • file that has contig, GO IDs


  • Big idea: For each of the six samples, map the reads to the GO IDs, see which GO IDs are over/underrepresented in the fed snakes. Follow those GO IDs to see which are of interest.
  • Approach one: most differentially expressed contig: associate most differentially expressed contigs with GO IDs look at associated functions. Do pairwise comparisons across snakes. Depth approach. Generates individual genes of interest.
  • Approach two: Get GO IDs for all contigs. Assign each GO ID a 'snake score. Pick out most different snake scores between fed and unfed snakes. Breadth approach. Generates large groups of genes involved in a function.

.results sheet: FPKM: normalized expression based on number of reads and length of gene

Back to home Dylan Maghini

      • Need to edit contig_to_GO file per Dr. C's requests. Also need to take out redundant GO IDs for each gene.