RiDE (RNA Differential Expression) is a pipeline for RNA-seq data analysis. The standardization provided by solida-core requires perhaps accessory user-defined files to have a given organization.
RiDE pipeline requires a single mandatory user input:
This file contains tab-separated information about samples to be analyzed and must be declared into the config.yaml file:
samples: "path_to_input_files/samples.tsv"
Samples file include information about sample IDs the absolute path of sequencing data file (or files if paired-end).
The file structure is described in the example below::
sample fq1 fq2
ERS179576 path_to_datasets/ERR174310_1.fastq.gz path_to_datasets/ERR174310_2.fastq.gz
ERS179577 path_to_datasets/ERR174324_1.fastq.gz path_to_datasets/ERR174324_2.fastq.gz
Where:
- sample: sample IDs;
- fq1-fq2: complete path and R1- and R2-fastq files (for paired-end sequencing).