RtABE_computational_analysis

This project provides relavant code for analyzing the efficiency and off-target effects of RtABE.

Author: Guo-Hua Yuan

Email: yuanguohua2020@sibs.ac.cn

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1. Features

• Editing Efficiency Calculation scripts_for_base_substitution_analysis: Evaluates RtABE editing efficiency at target sites with the deep sequencing data.
• Off-Target Effect Analysis scripts_for_RNA_editing_analysis: Detects potential off-target editing events with the whole-transcriptome sequencing data.

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2. Prerequisites

Before running this analysis, install the following tools:

• CFBI: https://github.com/YangLab/CFBI
• RADAR: https://github.com/YangLab/RADAR

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3. Usage

PART 1: Editing Efficiency Calculation

• Directory: scripts_for_base_substitution_analysis

  All original deep sequencing data used in this study can be accessed at the NCBI BioProject under the accession code PRJNA1115824. The provided code here serves as an example for reference.

• Constructing Index Files

  Before running the analysis, you need to construct index files. Refer to the index/ directory, which contains:

  • 20230927_deepseq_sample_name_mapping.csv:

    ID	Sample 1	Target site 1	Sample 2	Target site 2	...

  • ref_20230927.txt:

    Information
    Target site 1
    Sequence of target site 1
    Name of gRNA for target site 1: gRNA sequence 1
    None
    None
    Target site 2
    Sequence of target site 2
    Name of gRNA for target site 2: gRNA sequence 2
    None
    None
    ...

• Calculating Editing Efficiency

  Run

  sh CFBI_main.sh
  
  

PART 2: Off-Target Effect Analysis

• Directory: scripts_for_RNA_editing_analysis

  All original whole-transcriptome sequencing data used in this study can be accessed in the Gene Expression Omnibus under the accession codes GSE267726, in the Genome Sequence Archive of the BIG Data Center at the Beijing Institute of Genomics, Chinese Academy of Science under the accession codes HRA007429 and CRA016552, and in the National Omics Data Encyclopedia under the accession codes OEP00005360. The provided code here serves as an example for reference.

• Quality Control & Trim Reads

  Run

  sh work_QC_Trim.sh
  
  

• Whole-Transcriptome Off-Target Effect Analysis

  Run

  sh work_RADAR_parallel.sh
  
  

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4. Citation

Li G#, Chen G#, Yuan GH#, Wei J#, Ni Q, Wu J, Yang B, Yang L* and Chen J*. Specific and efficient RNA A-to-I editing through cleavage of an ADAR inhibitor. Nat Biotechnol, 2025 (Accepted in principle).