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Special Instructions for CAMBa Paper Review
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0. There are two other READMEs, one that mainly covers installation 
prerequisites and another that gives instructions for running the pipeline
itself.  A setup script will output additional instructions.  For the purposes 
of replicating the results in the paper, these instructions are too detailed, 
and the needed modifications are clarified in the following steps.

1. Of the programs mentioned in the "README-installation" file, to validate 
the experiments described in the paper, it is only necessary to have python2.6 
and Scipy installed.

2. Since the 'TillingN/' subdirectories and data files for the two experiments 
have already been provided, to run mutation detection on a specific TILLING 
experiment, it is necessary only to unarchive the corresponding .tar.gz data 
file within the "TILLING/" directory and to follow steps #2, #4, and #6 of the 
"README-pipeline" file.

3. Step #4 of "README-pipeline" will print another set of pipeline instructions.

Everything should already be set up correctly, so these instructions can be 
ignored, except for the two lines that say to make executable and then run 
"./generated_run_script_2.sh".  But before running 
"./generated_run_script_2.sh", the parameters for the current experiment must 
be uncommented in "find_mutations.py", as described below:

4. Before detecting mutations in Tilling3, uncomment the small parameter 
section with the Tilling3 parameters, on lines 97-103 of 
"find_mutations.py".  All similar parameter sections will be commented out.

Before detecting mutations in Tilling5, re-comment the parameter section for 
Tilling3 and uncomment the corresponding section for Tilling5, on lines 137-143.

5. A set of predictions across a range of thresholds will be stored within the
subdirectory "well_predictions_at_FrHq_thresh_0_std_and_nonstd" in the
directories Tilling3 and Tilling5.

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NOTE:
To avoid the time-consuming regeneration of the parsed MAQ pileup files, I have 
commented out lines 15-17 in "create_scripts.py", the only deviation from the 
standard pipeline.

The file "generated_run_script_2.sh" will also currently be set up to generate 
a set of statistics for the TILLING experiment, including coverage levels by 
gene and library.
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