Introduction

IPANEMAP suite workflow intend to provide automation in the data treatment of SHAPE Capillary Electrophoresis.

The workflow will enable you to generate structure data for a RNA fragment analysed using SHAPE with a set of conditions (Temperature, Magnesium, Probes.)

Tutorial

The usage of the software is as well described in the IPANEMAP Tutorial.

Example projects

We provide several example project directories with input, configuration and results.

• 01-SAM-I-aptamer-Bsubtilis

• 02-SAM-IV-aptamer-Mycobacterium

• 03-SAM-I-aptamer-Bsubtilis-footprint

• 3L0U

• 7OQC

• 3Q1A

• 6DNR

Integrated software

The software integrates

• QuShape

• IPANEMAP

• RNAFold

• VARNA.

• Custom scripts for file conversion, reactivity normalization and aggregation.

Note that all these requirements can be installed automatically.

Availability

The software source code is available at https://github.com/Sargueil-CiTCoM/ipasuite.

The source code for this documentation is available at https://github.com/Sargueil-CiTCoM/ipasuite-docs

Getting started

• Introduction
• Requirements
  • Operating system
• Installation
  • For Linux Systems:
  • For MacOS x64 Systems:
  • Basic usage
  • Update
  • Using a virtual machine (Windows users)
• Run the pipeline
  • Initialize your project
  • Configure your project
  • Run pipeline
  • In case of trouble :
  • Clean file
• Configuration
  • 1. Fill in config.yaml using ipasuite config
  • 2. Fill in samples.tsv
• Output and Reports
  • Normalized Reactivity
  • Aggregated Reactivity
  • Structures

Go further

• Data import
• Data conversion
• QuShape project generation
• QuShape treatment of SHAPE-CE data
• QuShape reactivity extraction
• Reactivity Normalization
  • Steps :
  • Simple normalization method
  • Interquartile method
• Reactivity Aggregation
• Structure generation - IPANEMAP
• Footprinting
• Workflow configuration reference
• Folder structure
• Troubleshooting
  • Rnasique fail on wayland.
  • Use of old qushape file
  • Runtime: Error validating config file.
• Pipeline scripts references
  • aggregate_reactivity
  • ceq8000_to_tsv
  • normalize_reactivity
  • qushape_extract_reactivity
  • qushape_proj_generator
  • footprint
  • shift_reactivity
  • split_fasta

Indices and tables

• Index

• Module Index

• Search Page