From 495228f7167a6df24a139022e7a0560a4dd07b56 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Wed, 26 Mar 2014 21:05:25 -0400 Subject: majorly rewrite and revamp the script to support runnign parts at a time --- README.md | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) (limited to 'README.md') diff --git a/README.md b/README.md index 18334c9..81f7fc6 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ Setup: Example Usage: - selectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta; + SelectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta; less PfalciparumGenome_HumanGenome/final_mers For user customizable variables: @@ -27,12 +27,21 @@ 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 + +By default SelectiveGenomeAmplification runs all four steps, but you can +specify the program to run other steps, like score in this example. + + current_run=run_1 SelectiveGenomeAmplification target.fasta bg.fasta score + +This function does not try to be smart, so use it wisely + ## Customizable variables range of mers, min and max variable | default | notes :---- | :---- | ---- | :---- +current\_run | Not Enabled | specify the run you want to run steps on min\_mer\_range | 6 | minimum mer size to use max\_mer\_range | 12 | maximum mer size to use max\_mer\_distance | 5000 | maximum distance between mers in foreground -- cgit v1.2.3