Automating Kmer Abundance Counts¶

Adrienne Hoarfrost, aka Lady Wizard was given an assignment to automate this task. She expertly executed and provided her files for you in her github repository.

On Fri, Aug 14, 2015 at 07:19:19PM -0400, C. Titus Brown wrote: Some of these files are good shotgun sequencing runs. Others are not. Which is which?

These are the raw sequencing data files:

Cartoons, when to automate:

Here are the steps to re-create Adrienne’s task:

Start AWS instance¶

Open an AWS instance and install the following packages (t2.micro is fine):

sudo apt-get update &&
sudo apt-get -y install git curl python-dev r-base-core r-cran-gplots

Make a directory called wand, then clone Lady Wizard’s github repository:

mkdir wand
git clone https://github.com/ahoarfrost/wand.git
cd wand

Her script files, with comments are located here:

After git clone, these files will be located in your directory /wand. Run do.sh

bash do.sh

After running, you should have this same resulting pdf:

kmer10hists.pdf

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