20.109(S17):Analyze RNA-seq data (Day7)
From Course Wiki
Introduction
Today you will analyze the RNA-seq data gathered from untreated DLD-1 and BRCA2- cells and etoposide treated DLD-1 and BRCA2- cells. Following RNA purification, the samples were submitted to the BioMicro Center for Illumina sequencing. Illumina sequencing technology, or sequencing by synthesis (SBS), is used for massively parallel sequencing with a proprietary method that detects single bases as they are incorporated into growing DNA strands.
Protocols
Analysis of RNA-Seq data by Amanda Kedaigle, Prof. Ernest Fraenkel & Prof. Leona Samson.
Erratum: On page 4, pheatmap (sampleDists, labels_row=filenames) should be replaced by pheatmap(sampleDists, labels_row=rownames(colData(dds))).
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