NTAP Download

Here we provide the downloading of NTAP program (R and Perl scripts) and two separated sample data sets. One of the sample data is from our lab and you can find the the details in this paper:

Li XY et al. (2008), High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression, The Plant Cell 20:259-276

Another dataset is downloaded from public microarry database GEO from NIH. The purpose is to demonstrate NTAP users how to analyze their own data step by step.

NTAP: The NTAP source code, R and Perl scripts. 
Sample Data 1: The rice histone modification data (~380k oligos/array).
Sample Data 2: The worm ChIP-chip data downloaded from GEO, with much more dense tiling (~2M oligos/array).

The usage of NTAP:

To try NTAP out by using provided Sample Data, please download the NTAP codes and either one of the two datasets. Extract NTAP_0.2.zip and then put the Sample Data zipped file into the NTAP directory, extract the Sample Data, override anything if indicated. Then open R and run the script in run.R file.

To use NTAP to analyze your own data, please prepare your input files, modify the parameters in the run.R file according to the instruction in the Help page.