HPC Module: RingMapper
Synopsis
Adds RingMapper and PairMapper to your environment
| About This Software | |
|---|---|
| Official Site | https://github.com/Weeks-UNC/RingMapper |
| Tags |
Installed Versions
| Version | Install Date | Default? |
|---|---|---|
| 1.1 | 2022-02-15 |
Description
RingMapper & PairMapper automate the detection of correlated modifcation events in mutational profiling (MaP) experiments.
RingMapper is a flexible code for computing correlations (RINGs) between all nucleotides in an RNA. Users can choose to compute correlations between single nucleotides (window=1; default) or between larger nucleotide windows (e.g. window=3, which tests whether 3-nt windows are correlated with each other). Run ringmapper.py with the --help flag for options.
PairMapper is a wrapper for RingMapper that performs PAIR-MaP analysis, i.e. it searches for correlations indicative of secondary structure base pairs. Correlation calculations are done using a 3-nt window and then filtered by nt complementarity and reactivity. Run pairmapper.py with the --help flag for options.
Both RingMapper and PairMapper require read alignment and preprocessing by ShapeMapper2 using the --output-parsed flag. See the ShapeMapper2 documentation for further information regarding alignment and processing options.
RING and PAIR-MaP data can be visualized using the arcPlot plotting tool.
Citation(s)
If you use RingMapper in your research, please cite:
- A.M. Mustoe, N.N. Lama, P.S. Irving, S.W. Olson, K.M. Weeks. RNA base-pairing complexity in living cells visualized by correlated chemical probing, PNAS (2019).
Category
| Library | Programming | Software | SysAdmin |
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