February 2, 2016

Classwork

Today in class, we shared group findings from January 28, 2016:

1. Blast the overrepresented sequences
   1. Blast groups found mostly mitochondrial or ribosomal genes.
   2. Intestine blast group found an amino transferase gene that may be of interest later.
   3. Liver blast group found an anti-hemorage gene that may be of interest later.

1. Attempt to access the list of genes (SRP-0151827) mentioned in the Andrew et al. (2015) study
   1. We can blast our sequences against the Andrew et al. (2015) library.
   2. We have the potential to download the entire library with instructions on the website, but do not understand how to use the software/programs required to do so.
   3. We found a toolkit that allows us to download one sequence at a time.
   4. We can blast within a run.

1. Add numbers to label proteins of "unknown function" in our reads
   1. Dylan and Dustin made a file that removed duplicate names from our runs.
   2. Dr. Campbell and Dr. Heyer used their file and got gene mapping results!

1. Normalize relative abundance of transcripts
   1. We used DEseq to normalize data.
   2. Data can be normalized using a total read count (TC) normalization.

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