From 30c4e85b59b59592b7db8ad2d22f63f7c279c8a6 Mon Sep 17 00:00:00 2001 From: Yaamini Venkataraman Date: Thu, 17 Nov 2016 10:34:47 -0800 Subject: [PATCH] Update README.md --- notebooks/README.md | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/notebooks/README.md b/notebooks/README.md index dfb1788..f1431e6 100644 --- a/notebooks/README.md +++ b/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