Example Files
Example scripts and data are included in the HiTRACE repository. For a new analysis, start with these example scripts and replace relevant values with yours:
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[NEW] For further practice, we provide 12 more examples. They are previous 1D and 2D datasets annotated by our experts. Download Script & Data, and follow these instructions.
Workspace files are provided for comparison only, when you want to double check if your results are the same (especially for Step #4). They are not needed for trying out and starting fresh.
Analysis Pipeline
The complete HiTRACE analysis pipeline is composed of the following steps.
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#0: Get Started
Checklist before kick off.
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#1: Load and Preview Data
Read in data and provide a quick look.
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#2: Further Alignment (optional)
Perform additional finer alignments.
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#3: Parameter Input
Input experiment details and basic RNA construct information.
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#4: Sequence Assignment
Annotate the position of each nucleotide position on the gel matching bands.
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#5: Peak Fitting
Integrate band intensities into nucleotide peak readings.
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#6: Data Corrections (for 1D data only)
Perform unsaturation, attenuation correction, background subtraction, and normalization for 1D data.
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#7: Error Estimates (for 1D data only)
Evaluate data and estimate errors across replicates.
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#8: Save your Work
Print well-annotated figures of your analysis for archiving.
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#9: Output RDAT File
Write analyzed result to file in RDAT format, for use of Z-score and prediction.
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#10: Calculate Z-score (for 2D data only)
Transfrom 2D chemical mapping data into Z-score for use as 2D pseudo-free energy bonus for RNAstructure.
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#11: Predict Secondary Structure
Run structural prediction using RNAstructure based on chemical mapping reactivity data, with bootstrapping for helix-wise confidence score.
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#12: Visualize Secondary Structure (optional)
Draw secondary structure using VARNA with nucleotides color-coded by reactivity, and mark difference between secondary structure models.
Bonus Graphic Tools
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Color 2D Diagram
Make publication-ready diagram of secondary structures with nucleotides color-coded by reactivity.
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Color 3D Model
Make publication-ready 3D models with nucleotides color-coded by reactivity.
Share your Data
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Submit to RMDB
Share your chemical mapping results to RNA Mapping Database.