README for MA2C
Time-stamp: <2008-06-02 14:06:26 Tao Liu>

* Install

Please check the file 'INSTALL' in the distribution.

* Usage

Usage: ma2c <tag file>

A sample tag file is included in the distribution, please check the
instruction there. To write a tag file, you should collect information
from the samplekey file from NimbleGen, and organize your design files
and data files.

* Output files

All the output files will be saved in a subdirectory named
'MA2C_Output/'.

1. For the given DESIGN_ID, MA2C will generate a tpmap file named
'MA2C_'+DESIGN_ID+'.tpmap'. Keeping this file in place will save time
while you run MA2C next time for the same DESIGN_ID.

2. For every CHIP_ID, MA2C generates a raw data , a normalized data
file and a R script file. The raw data file
('MA2C_'+CHIP_ID+'_raw.txt') can be reused if you keep it in
'MA2C_Output/'. But normalized data file --
'MA2C_'+CHIP_ID+'_normalized.txt'-- will never be reused. The R script
can be processed by R program to generate a pdf file visualizing the
normalized signal distribution for each CHIP_ID. A good ChIP
experiment must have a biased long right tail.

3. The peak regions output files include a bed file, a xls file, a
gzipped wig file and a FDR table together with its R script. These
file names are consistent with the file name for the tag file. BED
file can be loaded by UCSC genome browser or IGB which contains the
detected peak regions. XLS file provides more detailed information for
the regions. And the gzipped wig file represents the MA2Cscore values
along the chromosomes, which can be loaded by UCSC genome browser or
IGB from Affymetrix. To process the R script with FDR table in R will
generate a pdf figure. If the figure is like a log curve, the result
may be reliable.
