From 0d0678cc36f6c37c2e2802781b9b11662fe5735d Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Fri, 17 Jan 2014 22:25:51 -0500 Subject: update README.md --- README.md | 16 ++++++++-------- 1 file 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 -- cgit v1.2.3