Download MAT Library files according to
your own tiling array type
Make the .tag file
for your own project:
Here is a sample
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.
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
You can view the output
Affymetrix Integrated Genome Browser (IGB)
and the output ER.bed file
using UCSC Genome Browser.
Please see the
here for the BED file format. Two additional BED fields in MAT
If more than
70% of the ChIP-enriched region is annotated as repeats (either
we will add a 'R_' marker in the 4th column. For example, 'R_Si'
with 3 additional copies elsewhere in the genome. 'R' alone
means RepeatMasker repeats.
The 5th column
is the -10log10_pvalue (the higher the better) for each