Multi-dimensional Hybridization Pooling Experiment Setup

This tool can be used to design and generate the input files necessary for performing a multi-dimensional hybridization experiment. An example probes file can be found here: probes.txt. This example file is intended to be used with a 3-dimensional experiment using 5 pools per dimension. Use the Hybdecon software for manual calling of hits and deconvolution of the experiment. See below for further setup instructions.


Instructions
Before proceeding with the experiment, determine the number of dimensions required as well as the number of pools per dimension. The deconvolution script treats these dimensions as if they are dimensions on a coordinate system with X, Y and Z axes (for 3D experiments). So, for a 3-dimensional experiment with 5 pools per dimension, pools are named X1, X2, X3, X4, X5 in the X dimension, Y1, Y2, Y3, Y4, Y5 in the Y dimension and Z1, Z2, Z3, Z4, Z5 in the Z dimension.

This tool will assist in experiment setup by assigning probes to pools in such a way that no two probes (in a 3D pooling) are ever present in a pool more than twice, and no two probes (in a 2D pooling) are ever present in a pool more than once. Probes will be given a unique address such as (X1,Y1,Z1) or (X3,Y4,Z2), etc, indicative of the pools to which they belong. This method enables the deconvolution script to easily scale from 2D, 3D and beyond.

The number of probes in each experiment must be divisible evenly by the number of pools per dimension. In the case of a 3D experiment with 5 pools per dimension the number of probes required must be in multiples of 5.

Probes Input File
The probes file used as input should be a tab delimited file where the first column is a unique probe identifier used by the lab and the second column is the probe name. The first line should have the header as shown.
ID      Probe Name
1       rpl22_chestnut
2       CmSI0003
3       CmSI0006
4       CmSI0011
5       CmSI0013
6       CmSI0028
7       CmSI0033