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HPC Module: ShapeMapper

Synopsis

Adds ShapeMapper to your environment.

About This Software
Official Site https://github.com/Weeks-UNC/shapemapper2
Tags Biology, BioChem, Weeks-UNC, RNA, Parallel Sequencing

Installed Versions

Version Install Date Default?
2.1.5 2022-02-15

Description

ShapeMapper automates the calculation of RNA structure probing reactivities from mutational profiling (MaP) experiments, in which chemical adducts on RNA are detected as internal mutations in cDNA through reverse transcription and read out by massively parallel sequencing. ShapeMapper performs:

  • Reference sequence correction
  • Read basecall quality trimming
  • Paired read merging (using BBmerge)
  • Alignment to reference sequences (using bowtie2 or STAR)
  • Enforcement of read location requirements and primer trimming
  • Multinucleotide and ambiguously aligned mutation handling
  • Post-alignment basecall quality filtering
  • Chemical adduct location inference from detected mutations
  • Reactivity profile calculation and normalization

  • Heuristic quality control checks

  • Mutation rates calculation from mutation counts and effective read depths

Citation(s)

For ShapeMapper2 software, please cite:

  • Busan S, Weeks KM. Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2. RNA. 2018, 24(2):143-148.

For the MaP (mutational profiling) RNA adduct readout strategy, please cite either:

  • Siegfried NA, Busan S, Rice GM, Nelson JA, Weeks KM. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nat Methods. 2014, 11(9):959-65.

  • Smola MJ, Rice GM, Busan S, Siegfried NA, Weeks KM. Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat Protoc. 2015, 10(11):1643-69.

Category

Library Programming Software SysAdmin