update README.md

1 files changed, 8 insertions, 8 deletions

diff --git a/README.md b/README.md
index be20530..e491351 100644
--- a/README.md
+++ b/README.md
@@ -15,17 +15,17 @@ Setup:
     git clone git@github.com:mutantturkey/SelectiveGenomeAmplification.gi
     cd SelectiveGenomeAmplification
     make
+    sudo make install
 
 Example Usage:
 
-    cd SelectiveGenomeAmplification;
-    ./selectiveGenomeAmplification.sh PfalciparumGenome.fasta HumanGenome.fasta;
-    less PfalciparumGenome.fasta_HumanGenome_final_mers
-    
+    selectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta;
+    less PfalciparumGenome_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 
+    SelectiveGenomeAmplification.sh PfalciparumGenome.fasta half.fasta 
 
 ## Customizable variables
 
@@ -36,9 +36,9 @@ 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
+N | output_directory | $PWD/$foreground_$background/ | ex. if fg is Bacillus.fasta and  bg is HumanGenome.fasta then folder would be $PWD/Bacillus.fasta_HumanGenome_output.fasta/
+Y | counts_directory | $output_directory/.counts | directory for counts directory
+Y | tmp_directory=$output_directory/.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