pipeline_miRNA_seq

This pipeline performs miRNAseq mapping with STAR and counts mapped reads to STAR reference genome using STAR --quantmode TranscriptomeSAM GeneCounts as well counts mapped reads using featureCounts if a more specific GTF annotation file wants to be used.

Requirements

On top of the default CGAT setup, the pipeline requires the following.

Software: python (v3.8.12 with pysam v0.17.0 when built)
STAR (v2.7) featurecounts (v2.0.1) multiqc (v1.11)

Configuration

The pipeline requires a configured :file: pipeline.yml file.

Make a directory with your project name. Configure the pipeline with

python [path_to_repo]/pipeline_motif_analysis.py config

A pipeline.log and pipeline.yml file(s) will be added to your new directory. Modify the pipeline.yml according to your project.

Inputs

Trimmed unpaired fasta files ending in .fastq.gz
a STAR genome directory, pat hto be specified in pipeline.yml
a GTF adapted for featureCounts for miRNAs

Run pipeline

Run the pipeline with python [path_to_repo]/pipeline_miRNA_seq.py make full -v5.

Ouputs