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Jeffrey E Barrick

Jeffrey E Barrick

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Analyzing RNA-Seq data for differential gene expression

We will..In this exercise, we will analyze RNA-seq data for gene expression levels in a wild-type and mutant strain of Listeria.

Download data files

The data files for this example are in the path:

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File Name

Description

Sample

SRR034450.fastq

Single-end Illumina 36-bp reads

wild-type, biological replicate 1

SRR034451.fastq

Single-end Illumina 36-bp reads

ΔsigB mutant, biological replicate 1

SRR034452.fastq

Single-end Illumina 36-bp reads

wild-type, biological replicate 2

SRR034453.fastq

Single-end Illumina 36-bp reads

ΔsigB mutant, biological replicate 2

NC_017544.1.gbk

Reference Genome

Listeria monocytogenes strain 10403S

http://www.ebi.ac.uk/ena/data/view/SRP001753

http://www.biomedcentral.com/1471-2164/10/641

This data is from this paper:

Oliver, H.F., et al. (2009) Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. BMC Genomics 10:641. Pubmed

Install software

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You can view it in the ENA SRA here: http://www.ebi.ac.uk/ena/data/view/SRP001753

Install software

Bowtie

For RNA-seq analysis we're mainly counting the reads that align well, so we choose to use bowtie. (You could also use BWA or many other mappers).

Code Block
module load bowtie

Alternatively:

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Bioconductor modules for R statistics package
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