RNA-seq Bioinformatics

Introduction to bioinformatics for RNA sequence analysis

Compare DE genes across methods

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RNA-seq_Flowchart4

In this section we will compare the DE gene lists obtained from different DE methods (e.g. Ballgown, EdgeR, DESeq2)

Visualize overlap with a venn diagram. This can be done with simple web tools like:

Once you have run the DESeq2 tutorial, compare the sigDE genes to those saved earlier from ballgown and/or edgeR:

head $RNA_HOME/de/ballgown/ref_only/DE_genes.txt
head $RNA_HOME/de/htseq_counts/DE_genes.txt
head $RNA_HOME/de/deseq2/DE_sig_genes_DESeq2.tsv

Pull out the gene IDs

cd $RNA_HOME/de/

cut -f 1 $RNA_HOME/de/ballgown/ref_only/DE_genes.txt | sort | uniq > ballgown_DE_gene_symbols.txt
cut -f 2 $RNA_HOME/de/htseq_counts/DE_genes.txt | sort | uniq | grep -v Gene_Name > htseq_counts_edgeR_DE_gene_symbols.txt
cut -f 7 $RNA_HOME/de/deseq2/DE_sig_genes_DESeq2.tsv | sort | uniq | grep -v Symbol > DESeq2_DE_gene_symbols.txt

To get the two gene lists you could use cat to print out each list in your terminal and then copy/paste.

cat ballgown_DE_gene_symbols.txt
cat htseq_counts_edgeR_DE_gene_symbols.txt
cat DESeq2_DE_gene_symbols.txt

Alternatively you could view both lists in a web browser as you have done with other files. These two files should be here:

Example Venn Diagram (Two-way comparison: DE genes from StringTie/Ballgown vs HTSeq/DESeq2)


Example Venn Diagram (Three-way comparison: DE genes from StringTie/Ballgown vs HTSeq/DESeq2 vs HTSeq/EdgeR)


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