Differential gene expression analysis with voom-limma

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Reference no: EM13838916

Question: Please follow the steps and prepare a report with results of it.

Differential gene expression analysis

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1) FastQC A quality control application for high throughput sequence data

https://www.bioinformatics.babraham.ac.uk/projects/download.html
FastQC v0.11.3 (Win/Linux zip file)
FastQC v0.11.3 (Mac DMG image)

2) Differential gene expression analysis
refer to a case study from:
https://bioinf.wehi.edu.au/RNAseqCaseStudy/

Details:

a) short-read sequence alignment against chickpea genome
download chickpea genome annotation and assembly from: https://gigadb.org/dataset/100076
download and install an aligner, such as:

i) subread ( Linux and Mac OS X )

https://bioinf.wehi.edu.au/subread/

ii) Bowtie/Bowtie2 (unix and Mac OS)

iii) BWA ( Linux/Mac machine)

iv) SNAP Scalable Nucleotide Alignment Program

(for Windows, Linux and OS X)
https://snap.cs.berkeley.edu/

v) SOAPaligner Linux X86_64 or Mac OS X 10.6.3

references:
https://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/Alignment

https://en.wikipedia.org/wiki/List_of_sequence_alignment_software

b) Feature count

i) FeatureCount
https://bioinf.wehi.edu.au/featureCounts/

ii) HTseq
https://www-huber.embl.de/users/anders/HTSeq/doc/counting.html

c) Construct a data matrix and Differential gene expression analysis with voom-limma or edgeR

Reference no: EM13838916

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