From ff15f36a46617effd1ecb1dafb289c3c18cc836a Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Mon, 7 Apr 2014 12:52:49 -0400 Subject: Rename! --- README.md | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 9d52d27..18c0748 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -SelectiveGenomeAmplification +SelectiveWholeGenomeAmplification ============================ SWGA is a tool for choosing primers for the selective amplification of a @@ -42,21 +42,21 @@ To use this you'll need: ## Setup - git clone git@github.com:mutantturkey/SelectiveGenomeAmplification.git - cd SelectiveGenomeAmplification + git clone git@github.com:mutantturkey/SelectiveWholeGenomeAmplification".git + cd SelectiveWholeGenomeAmplification" make sudo make install ## Example Usage -Standard use of (SGA) SelectiveGenomeAmplification is easy. it takes two arguments, +Standard use of (SGA) SelectiveWholeGenomeAmplification" is easy. it takes two arguments, the foreground and background - SelectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta; + SelectiveWholeGenomeAmplification" PfalciparumGenome.fasta HumanGenome.fasta; less PfalciparumGenome_HumanGenome/final_mers ### SGA User Interface -SGA also comes with a easy to use user prompt called SelectiveGenomeAmplificationUI. +SGA also comes with a easy to use user prompt called SelectiveWholeGenomeAmplification"UI. It allows for a less experienced user to use SGA without issue. to run this all you need to do is run SelectiveGenomeAmiplifcationUI and you'll see a series of prompts asking the user about tunables like below @@ -69,7 +69,7 @@ SGA without issue. to run this all you need to do is run SelectiveGenomeAmiplifc Input the path to your foreground file:target.fa Input the path to your background file:humangenome.fa Would you like to output your inserted variables to a string you can later paste? (Y/N/Default=y): n - Run SelectiveGenomeAmplification? (Y/N/Default=y): y + Run SelectiveWholeGenomeAmplification"? (Y/N/Default=y): y ### Setting Tunable Parameters @@ -78,19 +78,19 @@ below. For user customizable variables, they need to be passed in as environmental variables like so: max_mer_distance=5000 max_select=6 min_mer_range=6 max_mer_range=12 \ - SelectiveGenomeAmplification.sh PfalciparumGenome.fasta half.fasta + SelectiveWholeGenomeAmplification".sh PfalciparumGenome.fasta half.fasta ### Running individual steps -By default SelectiveGenomeAmplification runs all four steps, but you can +By default SelectiveWholeGenomeAmplification" runs all four steps, but you can specify the program to run other steps, like in these examples. - current_run=run_1 SelectiveGenomeAmplification target.fasta bg.fasta score + current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta score - current_run=run_1 SelectiveGenomeAmplification target.fasta bg.fasta select score + current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta select score - current_run=run_1 SelectiveGenomeAmplification target.fasta bg.fasta 3 4 + current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta 3 4 valid steps are these: -- cgit v1.2.1