Update README.md

notebooks/README.md

@@ -15,7 +15,18 @@ This subdirectory hosts the Jupyter (iPython) notebooks that detail reproducible
 - Displays FastQC results from `2016-10-13-oly-gonad-OA-part-1.ipynb`
 
 [`2016-10-28-oly-gonad-OA-part-2-BLAST.ipynb`](https://github.com/yaaminiv/yaaminiv-fish546-2016/blob/master/notebooks/2016-10-28-oly-gonad-OA-part-2-BLAST.ipynb)
-- Ran BLAST of draft *O. lurida* transcriptome against specialized Uniprot database (in progress as of 2016-11-04, to be completed by 2016-11-07).
+- Ran BLAST of draft *O. lurida* transcriptome against specialized Uniprot database that includes gene ontology information
+- Updated blastx arguments to rerun blastx and produce only best matches with Uniprot database
 
 [`2016-11-04-oly-gonad-OA-kallisto.ipynb`](https://github.com/yaaminiv/yaaminiv-fish546-2016/blob/master/notebooks/2016-11-04-oly-gonad-OA-part3-kallisto.ipynb)
-- Ran Kallisto to get count data (in progress as of 2016-11-04, to be completed by 2016-11-07).
+- Ran Kallisto to get count data
+
+[`2016-11-11-oly-gonad-OA-part4-differential-expression.ipynb`](https://github.com/yaaminiv/yaaminiv-fish546-2016/blob/master/notebooks/2016-11-11-oly-gonad-OA-part4-differential-expression.ipynb)
+- Took count data and ran through DESeq2
+- Identified genes differentially expressed at different levels of significance
+- Compared the following sets:
+ - All .fastq files
+ - Female_106 vs. Female_108
+ - Male_106 vs. Male_108
+ - Female_106 vs. Male_106
+ - Female_108 vs. Male_108