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How to generate heatmaps for RNA-Seq data

This recipe generates a heatmap for differential expression data

1 result • updated 5.0 years ago by Istvan Albert

This recipe generates a heatmap for differential expression data

For more information see the

Bioinformatics Data Analysis online course.
Biostar Handbook for system setup and other information.

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# Print commands to standard output.
set -uex

# The R code in this recipe assumes
# that the Deseq1, Deseq2 and edgeR methods have been
# installed with Bioconductor.

# Obtain the three data analysis scripts.
wget -q -nc http://data.biostarhandbook.com/rnaseq/code/deseq1.r
wget -q -nc http://data.biostarhandbook.com/rnaseq/code/deseq2.r
wget -q -nc http://data.biostarhandbook.com/rnaseq/code/edger.r

# Get the RNA-Seq count table as input data.
wget -q -nc http://data.biostarhandbook.com/rnaseq/code/counts.txt

# Analyze the counts with DESeq1.
cat counts.txt | Rscript deseq1.r 3x3 > results_deseq1.txt 2>> log.txt

# Analyze the counts with DESeq2.
cat counts.txt | Rscript deseq2.r 3x3 > results_deseq2.txt  2>> log.txt

# Analyze the counts with EdgeR.
cat counts.txt | Rscript edger.r 3x3 > results_edger.txt  2>> log.txt

# Download the script to draw the heatmaps (requires the glplots package).
wget -q -nc http://data.biostarhandbook.com/rnaseq/code/draw-heatmap.r

# Generate heatmap from the deseq1 normalized matrix.
cat norm-matrix-deseq1.txt | Rscript draw-heatmap.r > heatmap-norm-matrix-deseq1.pdf  2>> log.txt

# Generate heatmap from the deseq2 normalized matrix.
cat norm-matrix-deseq2.txt | Rscript draw-heatmap.r > heatmap-norm-matrix-deseq2.pdf  2>> log.txt

# Generate heatmap from the edgeR normalized matrix.
cat norm-matrix-edgeR.txt | Rscript draw-heatmap.r > heatmap-norm-matrix-edgeR.pdf  2>> log.txt

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[settings]
id = 66
recipe_uid = "recipe-heatmap"
uid = "recipe-heatmap"
name = "How to generate heatmaps for RNA-Seq data"
template = "How_to_generate_heatmaps_for_RNA-Seq_data_bio-data-analysis_66.sh"
image = "How_to_generate_heatmaps_for_RNA-Seq_data_bio-data-analysis_66.png"
project_uid = "bio-data-analysis"
url = "http://localhost8000"
help = "This recipe generates a heatmap for differential expression data\n\nFor more information see the\n\n* [Bioinformatics Data Analysis][link]  online course.\n* [Biostar Handbook][book] for system setup and other information.\n\n[link]: https://www.biostarhandbook.com/edu/course/4/\n[book]: https://www.biostarhandbook.com"

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