Probe Design

This guide provides a walkthrough of how to design molecular inversion probes (MIPs) using MIPTools. We use a test data set to demonstrate each step in the design process.

Download Test Data

The test data set can be downloaded here or via the use of the command line:

# Download and untar directory
wget -qO- https://baileylab.brown.edu/MIPTools/download/test-data.tar.gz | tar -xvz

The test data set contains 5 directories that contain the test data, species resources, as well as project resources:

tree -FL 1 test-data

#> test-data
#> ├── DR1_project_resources/
#> ├── hg38_host/
#> ├── pf_species_resources/
#> ├── test_data/
#> └── test_design_resources_pf/

Test designs will be carried out on a few Plasmodium falciparum targets. The species resources directory includes resources for the P. falciparum genome and the host resources directory contain the resources for the human genome, which will be used as the host species.

Attention

The MIP design manual can be found here, for the time being, and an example walkthrough here. We plan on merging those documents here in the future…