Small Demo - Oshlack/necklace GitHub Wiki

Here we provide a small example to demonstrate and test your installation of necklace. It should take about an hour or so to run and includes a subset of the read data from this public RNA-Seq dataset (which explores gene expression in lactating sheep). In the example we just look at genes and reads from sheep chromosome 14 using human chromosome 19 as our related species genome.

1. Download and install necklace.

2. Download the sheep demo data files (about 56MB) and untar: tar -zxvf sheep_small_demo_data.tar.gz

3. Run necklace using the file data/data.txt: <path_to_necklace>/tools/bin/bpipe run <path_to_necklace>/necklace.groovy data/data.txt

4. Take a look at the output to see what necklace produces and check that it's completed properly.

Please report any issues you have to us.