Step-by-step instructions:

1. Download and install MAT

2. Download MAT Library files according to your own tiling array type

3. Make the .tag file for your own project:
   Here is a sample Tag file and raw data for Estrogen Receptor (ER) ChIP-chip on Affymetrix Chromosomes 21 and 22 arrays. Please make your own tag file (plain-text with a .tag suffix) according to this example using any plain-text editor.

4. Running MAT by typing 'MAT tag_files'. You can even specify multiple tag files to MAT. You should be able to run MAT on the above ER raw data.

5. You can view the output ER.bar files using Affymetrix Integrated Genome Browser (IGB)
   and the output ER.bed file using UCSC Genome Browser.

6. Please see the here for the BED file format. Two additional BED fields in MAT are:

   1. If more than 70% of the ChIP-enriched region is annotated as repeats (either RepeatMasker repeats or simple repeats or segmental duplication), we will add a 'R_' marker in the 4th column. For example, 'R_Si' means simple repeats, 'R_Se3' means segmental duplication with 3 additional copies elsewhere in the genome. 'R' alone means RepeatMasker repeats.

   2. The 5th column is the -10log10_pvalue (the higher the better) for each ChIP-enriched region.