GeneNoteBook test data

To quickly test GeneNoteBook functionality, the GeneNoteBook repository contains a small test dataset of 100 genes from Medicago truncatula, along with predicted protein domains and quantified gene expression from several publicly available transcriptomes.


Download testdata

wget https://github.com/genenotebook/genenotebook/raw/master/testdata.tgz &&\
tar xvxzf testdata.tgz

Load test data into running GeneNoteBook daemon

Run the following commands from the testdata folder


Add reference genome

genenotebook add genome -u admin -p admin -n test testdata.fasta

Add gene annotations

genenotebook add annotation -u admin -p admin -n test testdata.gff3

Add InterProScan protein domain predictions

genenotebook add interproscan -u admin -p admin testdata.iprscan.gff3 

Add transcriptomes

find . -name "*abundance.tsv" |\
xargs -n 1 -P 1 -I % sh -c "genenotebook add transcriptome -u admin -p admin %"