Add variables to readme.markdown

1 files changed, 32 insertions, 3 deletions

diff --git a/README.md b/README.md
index 27885f0..55acf5d 100644
--- a/README.md
+++ b/README.md
@@ -1,12 +1,41 @@
 SelectiveGenomeAmplification
 ============================
 
-http://brisson.bio.upenn.edu/
+PI: http://brisson.bio.upenn.edu/
 
-To Use this you'll need:
+To use this you'll need:
 
  - A unix environment
  - kmer_total_count, a kmer counter available here: http://github.com/mutantturkey/dna-utils/
  - bash or compliant shell.
  
-  
+ 
+
+Example Usage:
+
+    cd SelectiveGenomeAmplification;
+    ./selectiveGenomeAmplification.sh PfalciparumGenome.fasta HumanGenome.fasta;
+    less PfalciparumGenome.fasta_HumanGenome_final_mers
+   
+For user customizable variables:
+
+    max_mer_distance=5000; max_select=6 min_mer_range=6 max_mer_range=12 \
+    ./SelectiveGenomeAmplification.sh PfalciparumGenome.fasta half.fasta 
+
+## Customizable variables
+
+range of mers, min and max 
+
+C | variable | default | notes
+:---- | :---- | :---- | ---- | :----
+Y | min_mer_range | 6  | minimum mer size to use
+Y | max_mer_range | 10 | maximum mer size to use 
+Y | max_mer_distance | 5000 | maximum distance between mers in foreground
+Y | counts_directory | $PWD/counts | *PWD is current directory
+N | output_directory | $PWD/$foreground_$background/ | ex. if fg is Bacillus.fasta and  bg is HumanGenome.fasta then folder would be $PWD/Bacillus_HumanGenome_output/
+Y | tmp_directory=$PWD/tmp | temporary files directory
+Y | max_melting_temp | 30° | maximum melting temp of mers
+Y | min_melting_temp | 0° | minimum melting temp of mers
+Y | min_mer_count | Not Enabled (0) | only select mers that occur more frequently than this number
+Y | max_select | maximum number of mers to pick
+Y | ignore_mers | Not Enabled | mers to explicitly ignore, space seperated ex. ignore_mers="ACAGTA ACCATAA ATATATAT"