RNA seq analysis with reference genome

RNA seq analysiswith reference genome

Dataset • Reference genome • mouse chromosome 16 subset, 13Mbp (complete chr16, 98Mbp) • Reads • Brain • Liver Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by rna-seq. Nat Methods, 5(7):621-628.

Import Genome information • NC000082subset.gbk

Start RNA seq analysis

Select Reference with annotation

Setting mapping argument

setting Exon argument

RPKM • Read per kilobase of exon model per million mapped reads • # total mapped reads • Mapped contig/exon length Mortazavi, A. et.al. (2008). Mapping and quantifying mammalian transcriptomes by rna-seq. Nat Methods, 5(7):621--628.

Exercise: • Import Liver Reads • do above steps

Expression analysis

Experiment Table for Comparision

Comparative analysis for denovotranscriptome analysis?

RNA seq analysis with reference genome

RNA seq analysis with reference genome

Presentation Transcript

RNA-Seq

RNA-Seq and transcriptome analysis

RNA- seq Analysis

RNA- Seq Lab

Measuring transcriptomes with RNA-Seq

RNA seq (I)

Le RNA-seq

Finding genes de novo with RNA- seq

RNA- seq Analysis Practical Exercise

Statistics for RNA- seq Analysis

RNA-Seq and transcriptome analysis

Comparative analysis of RNA- Seq data with DESeq and DEXSeq

RNA-seq data

RNA-Seq datasets

Bioinformatics Pipelines for RNA- Seq Data Analysis

RNA- seq Analysis in Galaxy

Applications of RNA-Seq

Uncovering the Popularity of RNA Seq Analysis

RNA-SEQ