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@@ -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 |