Dataset S1 - ScanFold and Reactivity analyses

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Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Program, Pipeline Name or Method Name: 
SHAPE, DMS, ScanFold
Program, Pipeline or Method version: 
SHAPE, DMS, ScanFold
Source Name: 
Time Executed: 
Materials & Methods (Description and/or Program Settings): 
Supplemental Data Set 1 for "A map of the SARS-CoV-2 functional RNA Structurome" In Supplemental Data Set 1, there are two directories, "ScanFold Scans" and "Reactivity and Scan Analyses". The "ScanFold Scans" directory contains several internal directories with the in silico and constrained ScanFold output files for each model condition. The internal directories also contain the constraint files used for each associated run. The "Reactivity and Scan Analyses" contains 4 excel documents used to analyze the reactivity values/hard constraints and resulting ScanFold outputs. ScanFold_Metric_analysis.xlsx: Contains analyses and comparisons of in silico and top 10% constrained scan output ScanFold_Constraint_Conflict.xlsx: This file compares the top 10% of hard constraints from each dataset with in silico ScanFold predictions and reports positions where hard constraints and predicted base pairs conflict SHAPE_and_DMS_Constraint_Comparison.xlsx: Has the top 10% (and 20%) of hard constraints used from each experimental data set and compares their location/distribution in the genome. Also contains reactivitie ranges for the top 10% of SHAPE values. ScanFold_bp_Comparisons.xlsx: Contains comparisons of in silico and constrained .bp files and reports similarity of structure (both paired and unpaired) between the files. Sensitivity and PPV are also calculated here. All excel files contain additional information and descriptions of data.
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