Generation Information and Q&A
What is the purpose of data simulation/in silico digestion of sequence?
To create in silico map from sequences
- to estimate the labelling density before experiment for choosing enzymes
- to align to optical maps obtained from experiments
Decide what enzyme to use
Suppose you have 2 enzymes available: BbvCI and BspQI, and you want to test which one is best for your experiment. The general flow is to do the in-silico digestion, and check for the signal density with DataStatistics module, and visualize them in OMView.
Quick commands
java -jar OMTools.jar FastaToOM --fastain Sample.fa --refmapout Sample_BbvCI.cmap --enzyme BbvCI
java -jar OMTools.jar FastaToOM --fastain Sample.fa --refmapout Sample_BspQI.cmap --enzyme BspQI
java -jar OMTools.jar DataStatistics --optmapin Sample_BbvCI.cmap Sample_BspQI.cmap --statout SampleEnzymeStat.txt
java -jar OMTools.jar DataTools --optmapin Sample_BbvCI.cmap --optmapout Sample_rename_BbvCI.cmap --idprefix BbvCI_
java -jar OMTools.jar DataTools --optmapin Sample_BspQI.cmap --optmapout Sample_rename_BspQI.cmap --idprefix BspQI_
cat Sample_rename_BbvCI.cmap Sample_rename_BspQI.cmap > combined.cmap
java -jar OMTools.jar OMView --optmapin combined.cmap --viewmolecule true