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Diffstat (limited to 'README.md')
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1 files changed, 46 insertions, 5 deletions
@@ -3,6 +3,9 @@ SelectiveGenomeAmplification PI: http://brisson.bio.upenn.edu/ + + +## Requirements To use this you'll need: - A unix environment @@ -10,31 +13,69 @@ To use this you'll need: - bash or compliant shell. -Setup: +## Setup git clone git@github.com:mutantturkey/SelectiveGenomeAmplification.git cd SelectiveGenomeAmplification make sudo make install -Example Usage: +## Usage Examples +Standard use of (SGA) SelectiveGenomeAmplification is easy. it takes two arguments, +the foreground and background + SelectiveGenomeAmplification PfalciparumGenome.fasta HumanGenome.fasta; less PfalciparumGenome_HumanGenome/final_mers -For user customizable variables: +SGA allows for many tunable parameters, which are all explained in the chart +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 +SGA also comes with a easy to use user prompt called SelectiveGenomeAmplificationUI. +It allows for a less expereienced user to use +SGA without issue. + +### Running individual steps By default SelectiveGenomeAmplification runs all four steps, but you can -specify the program to run other steps, like score in this example. +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 SelectiveGenomeAmplification target.fasta bg.fasta select score + + current_run=run_1 SelectiveGenomeAmplification target.fasta bg.fasta 3 4 + +valid steps are these: + +- count (1) +- filter (2) +- select (3) +- score (4) + This function does not try to be smart, so use it wisely + +### Manually scoring mer combinations + +Users can manually score combinations of mers they choose using the +score\_mers.py script. + + score_mers.py -f foreground.fa -b background.fa -c combination file -o output + + +The combination file should look like this: + + ACGATATAT TACATAGA TATATATAT ACGTACCAT ATATTA + AAATTATCAGT ATACATA ATATACAT ATATACATA ACATA + ATATACATA ATCATGATA CCAGATACATAT + +each row is combination to be scored. + ## Customizable variables range of mers, min and max @@ -45,7 +86,7 @@ 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 -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/ +output\_directory | $foreground\_$background/ | ex. if fg is Bacillus.fasta and bg is HumanGenome.fasta then folder would be $PWD/Bacillus.fasta\_HumanGenome\_output.fasta/ counts\_directory | $output\_directory/.tmp | directory for counts directory tmp\_directory | $output\_directory/.tmp | temporary files directory max\_melting\_temp | 30° | maximum melting temp of mers |