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Bioinformatics for Transcriptome Analysis

Exercises for transcriptome analysis workshop taught at UNAM-Morelia, Mexico in January 2019. Topics include Linux basics, Illumina data quality assessment, quantifying gene expression levels with RNA-Seq, testing for differential expression among experimental treatments, and weighted gene coexpression network analysis.

Required software

On local computer

Windows: PuTTY and FTP client (e.g., FileZilla or WinSCP)

MacOs: FTP client (e.g., FileZilla)

On server

bowtie2

samtools

fastq_screen

fastqc (see "Requirements" section for dependencies)

R (optionally with RStudio)

Then in R, run the following commands to install necessary packages (and any dependencies):

install.packages(c("gplots", "pheatmap", "RColorBrewer", "igraph"))
if (!requireNamespace("BiocManager"))
  install.packages("BiocManager")
BiocManager::install()
BiocManager::install(c("qvalue", "DESeq2", "WGCNA", "Rsubread", "genefilter"))

Trimmomatic

STAR