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| -rw-r--r-- | README.md | 31 |
1 files changed, 16 insertions, 15 deletions
@@ -15,7 +15,7 @@ PI: http://brisson.bio.upenn.edu/ * [Requirements](#requirements) * [Setup](#setup) * [Example Usage](#example-usage) - * [SGA User Interface](#sga-user-interface) + * [SWGA User Interface](#sga-user-interface) * [Setting Tunable Parameters](#setting-tunable-parameters) * [Running Individual Steps](#running-individual-steps) * [Manually Scoring Specific Mer Combinations From List ](#manually-scoring-specific-mer-combinations-from-list) @@ -42,23 +42,24 @@ To use this you'll need: ## Setup - git clone git@github.com:mutantturkey/SelectiveWholeGenomeAmplification".git - cd SelectiveWholeGenomeAmplification" + git clone git@github.com:mutantturkey/SelectiveWholeGenomeAmplification.git + cd SelectiveWholeGenomeAmplification make sudo make install ## Example Usage -Standard use of (SGA) SelectiveWholeGenomeAmplification" is easy. it takes two arguments, +Standard use of (SGA) SelectiveWholeGenomeAmplification is easy. it takes two arguments, the foreground and background - SelectiveWholeGenomeAmplification" 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 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 +### SWGA User Interface +SWGA also comes with a easy to use user prompt called SelectiveWholeGenomeAmplificationUI. +It allows for a less experienced user to use SWGA 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 Where would you like to temporary files to be stored? (Default=$output_directory/.tmp): Where would you like to count files to be stored? (Default=$output_directory/.tmp): @@ -69,7 +70,7 @@ 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 SelectiveWholeGenomeAmplification"? (Y/N/Default=y): y + Run SelectiveWholeGenomeAmplification? (Y/N/Default=y): y ### Setting Tunable Parameters @@ -78,19 +79,19 @@ 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 \ - SelectiveWholeGenomeAmplification".sh PfalciparumGenome.fasta half.fasta + SelectiveWholeGenomeAmplification.sh PfalciparumGenome.fasta half.fasta ### Running individual steps -By default SelectiveWholeGenomeAmplification" 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 SelectiveWholeGenomeAmplification" target.fasta bg.fasta score + current_run=run_1 SelectiveWholeGenomeAmplification target.fasta bg.fasta score - current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta select score + current_run=run_1 SelectiveWholeGenomeAmplification target.fasta bg.fasta select score - current_run=run_1 SelectiveWholeGenomeAmplification" target.fasta bg.fasta 3 4 + current_run=run_1 SelectiveWholeGenomeAmplification target.fasta bg.fasta 3 4 valid steps are these: |