- Download the source code and place it into a folder called OPTIMA, inside a
main folder ('main_folder').
- Download the jar dependencies and place them into the main folder.
- Download the sample maps (simulated from GRCh37/hg19 human reference
genome, scenario (A), KpnI restriction enzyme) into the main folder: maps.
- Download GRCh37/hg19 human reference genome in in silico format (KpnI
restriction enzyme) into the main folder: reference.
- From the main folder, compile the Java source code:
javac OPTIMA/Align.java
- Run (in one command line only):
java OPTIMA/Align Human-scenarioA-KpnI_sample.maps sample_output
Human_reference_hg19-KpnI.silico pvalue allMaps >sample_output.log
- The solution can be found in locations.
- For output analysis and interpretation, please refer to the source code
manual on GitHub: manual.
- For Linux, UNIX and MacOS X users, please run from the main folder:
javac -cp ".:cern.jar:commons-math3-3.2.jar" OPTIMA/Align.java
java -cp ".:cern.jar:commons-math3-3.2.jar" OPTIMA.Align
Human-scenarioA-KpnI_sample.maps sample_output
Human_reference_hg19-KpnI.silico pvalue allMaps >sample_output.log
- For Windows users, please run from the main folder:
javac -cp ".;cern.jar;commons-math3-3.2.jar" OPTIMA/Align.java
java -cp ".;cern.jar;commons-math3-3.2.jar" OPTIMA.Align
Human-scenarioA-KpnI_sample.maps sample_output
Human_reference_hg19-KpnI.silico pvalue allMaps >sample_output.log
- In case you would like to run the program from a different folder,
just change the running path to include the main folder; e.g. for Unix:
java -cp "main_folder:main_folder/cern.jar:main_folder/commons-math3-3.2.jar"
OPTIMA.Align Human-scenarioA-KpnI_sample.maps sample_output
Human_reference_hg19-KpnI.silico pvalue allMaps >sample_output.log
- Our map input format in already in one of the two output formats provided by
the OpGen Argus system.
For in silico restriction sites conversion of FASTA sequences, please see our
script repository.
Scripts for converting BioNano Genomics Irys platform data to our input
format can be found here.