rnaseq-pipeline

A nextflow pipeline for aligning, mapping & estimating abundances of RNASeq data (.bam files). The following are the components of the pipeline:

1. STAR
2. regtools
3. stringtie
4. intron_analysis

Prerequisites

Install nextflow and docker CE.

Building

git clone https://github.com/YounisLab/splicing-analysis
cd splicing-analysis
docker image build -t splicing-analysis .
cd ../
git clone https://github.com/YounisLab/rnaseq-pipeline
cd rnaseq-pipeline
docker image build -t rnaseq-pipeline .

Running

Usage: nextflow run rnaseq-pipeline.nf [OPTIONS] --ref_dir <REF_DIR> --fastq_dir <FASTQ_DIR> --star_index <STAR_INDEX_DIR> --genome <GENOME_VERSION> --cores <NUM_CORES> --output_dir <OUTPUT_DIR>
    Mandatory args:
        <REF_DIR>         Directory containing reference files
        <FASTQ_DIR>       Directory containing .fastq file(s) to run through the pipeline.
                          Unless --single_end is specified, files in this directory
                          must be of the form '<SAMPLENAME>_[A-Z]_R{1,2}.fastq',
                          where [A-Z] refers to statistical replicates and R{1,2} refers to paired-ends.

                            Example:
                                SAMPLE_A_R1.fastq SAMPLE_A_R2.fastq SAMPLE_B_R1.fastq SAMPLE_B_R2.fastq

                                This will be run in STAR as:
                                --readFilesIn SAMPLE_A_R1,SAMPLE_B_R1.fastq SAMPLE_A_R2.fastq,SAMPLE_B_R2.fastq

                          Here 'SAMPLE_A_R1.fastq' and 'SAMPLE_A_R2.fastq' are paired end reads, while
                          'SAMPLE_A_R1.fastq' and 'SAMPLE_B_R1.fastq' are statistical replicates
                          belonging to the same paired end read.

        <STAR_INDEX_DIR>  Directory containing STAR indices
        <GENOME_VERSION>  Human Genome version prefix used in REF_DIR files
        <NUM_CORES>       Number of CPU cores to use in pipeline.
        <OUTPUT_DIR>      Directory to save output from pipeline.

    Optional args ([OPTIONS]):
        --single_end      Specifies that the --fastq_dir input contains single end reads only.
                          If enabled, files in the --fastq_files directory must be of the form
                          '<SAMPLENAME>_[A-Z].fastq', where [A-Z] refers to statistical replicates.

                            Example:
                                SAMPLE_A.fastq SAMPLE_B.fastq SAMPLE_C.fastq SAMPLE_D.fastq

                          This will be run in STAR as:
                          --readFilesIn SAMPLE_A.fastq,SAMPLE_B.fastq,SAMPLE_C.fastq,SAMPLE_D.fastq

        --no_replicates   Specifies that each .fastq file in the input directory
                          should be run through the pipeline individually.