Folder structure

Your project should be organized the following way :

├── config
│   ├── config.yaml
│   └── samples.tsv
├── resources # Contains input files
│   ├── 1.1-fluo-ceq8000 # SHAPE data from ceq8015
│   ├── 1.2-fluo-ce # SHAPE data in a tsv format readable by QuShape
│   ├── sequence1.fa # Reference sequences of the studied RNA
│   ├── ... 
│   └── sequenceN.fa
├── results # Intermediary and analysed data
│   ├── 2-qushape
│   ├── 3.1-reactivity
│   ├── 3.2-normreact
│   ├── 4.1-aggreact
│   ├── 4.2-aggreact-ipanemap
│   ├── 5.1-ipanemap-config
│   ├── 5.2-ipanemap-out
│   ├── 5.4-varna 
│   └── 5.5-footprint
└── workflow # Scripts used for data treatement

config

This folder contains the two main configuration files: config.yaml Which contains general configuration of the pipeline and samples.tsv Which contains informations about each sample

resources

Folder containing input files. Those file can be imported from external folder using probe_file and control_file fields in samples.tsv or you can directly add file naming them using the schema in config.yaml->format->[control_]condition sequences files can have abritrary name, since they must be declared in config.yaml in the sequences section.

1.1-fluo-ceq8000

Raw sequencing data in the original ceq8015 format

1.2-fluo-ce

Sequencing data in a tsv format readable by QuShape

results

Contains intermediary and final results from data treatement.

2-qushape

Contains qushape projects. Those project can be generated automatically by the pipeline or imported using qushape_file field in samples.tsv.

3-reactivity

Contains reactivity extracted automatically from qushape project, once the have been analysed

3.2-normreact

Contains Normalized reactivity

4.1-aggreact

Contains aggregated reactivity : each replicate with the same conditions are aggregated together

5.3-structure

Secondary structures generated by IPANEMAP in .dbn format

5.4-varna

Secondary structures generated by IPANEMAP in .varna format

5.5-footprint

Footprint analysis pairwisely comparing experiments