Using another program

Once the data have been extracted using NMcl2tab, the outputed file can be directly used by other softwares, in particular by TileMap (3) which is available at http://biogibbs.stanford.edu/~jihk/TileMap/index.htm. Normalization can then be done by using the program tilemap_norm from the TileMap package (note that this program implements only a quantile normalization).

We provide in the directory Data/BY_S288c/Array/ a template of the configuration file required by tilemap_norm to run:

$cat Data/BY_S288c/Array/NucOccupancy.norm
###############################
# TileMap Normalization       #
###############################

[Working directory] = .
[Raw Data file]     = NucOccupancy_raw.txt
[Export file]       = NucOccupancy_norm.txt
[Array number]      = 3
[Truncation lower bound before normalization] = -1000000000.0
[Take log2 transformation before normalization] (1:yes; 0:no) = 1

We invite you to have a look at the TileMap manual to have more details on this file. Finally, the normalization can be done like this (assuming that you have previously added to your $PATH variable the location of the TileMap binaries):

$cd Data/BY_S288c/Array/
$tilemap_norm NucOccupancy.norm

You then should have a new file in Data/BY_S288c/Array/ called NucOccupancy_norm.txt that have the same format than NucOccupancy_raw.txtbut for which the hybridization intensities have been normalized.