February 2, 2016

Classwork

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

1. Blast the overrepresented sequences

• Blast groups found mostly mitochondrial or ribosomal genes.
• Intestine blast group found an amino transferase gene that may be of interest later.
• 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

• We can blast our sequences against the Andrew et al. (2015) library.
• 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.
• We found a toolkit that allows us to download one sequence at a time.
• We can blast within a run.

1. Add numbers to label proteins of "unknown function" in our reads

• Dylan and Dustin made a file that removed duplicate names from our runs.
• Dr. Campbell and Dr. Heyer used their file and got gene mapping results!

1. Normalize relative abundance of transcripts

• We used DEseq to normalize data.
• Data can be normalized using a total read count (TC) normalization.

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