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