RNA-Seq DE analysis summary

RNA-Seq with Bioconductor in R

Mary Piper

Bioinformatics Consultant and Trainer

workflow

RNA-Seq with Bioconductor in R

RNA-Seq prep

RNA-Seq with Bioconductor in R

QC

RNA-Seq with Bioconductor in R

RNA-Seq Workflow: Raw data quality control

Sequence contamination

RNA-Seq with Bioconductor in R

Alignment

RNA-Seq with Bioconductor in R

RNA-Seq Workflow: Alignment

Alignment2

RNA-Seq with Bioconductor in R

Quantitation

RNA-Seq with Bioconductor in R

RNA-Seq Workflow: Quantitation

counts

RNA-Seq with Bioconductor in R

Full workflow

RNA-Seq with Bioconductor in R

Preparation for differential expression analysis: DESeq2 object

dds <- DESeqDataSetFromMatrix(countData = rawcounts,
                        colData = metadata,
                        design = ~ condition)

counts data

RNA-Seq with Bioconductor in R

Let's practice!

RNA-Seq with Bioconductor in R

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