Difference between revisions of "DM Notes 3.8.16"
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What have we done so far? | What have we done so far? | ||
| − | * | + | * file that has organism, contig, GO IDs associated |
| + | * file that has contig, GO IDs | ||
| + | Directions: | ||
| + | * 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]] | 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. | ||
Latest revision as of 23:46, 9 March 2016
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
Directions:
- 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.
