README.md

pipeline_salmonquant

The pipeline performs the following:

• Uses gff2fasta to convert a .gtf formatted geneset into a FASTA format, building a transcriptome.
• Builds a salmon index from the FASTA formatted transcriptome generated
• Quantifies .fastq formatted RNA-seq reads and
• Generates gene expression estimates (TPM and counts) at the transcript and gene level, using Salmon as an alignment-free expression estimation.

Inputs needed

1. A geneset in a .gtf format. Unzip .gtf.gz files before running the pipeline_salmonquant.
2. RNA-seq reads in .fastq.gz format

For accessing the pipeline through cgatflow command

Clone/download the repository

Copy the pipeline_salmonquant.py and pipeline_salmonquant folder to your cgat/cgat-flow/CGATPipelines/.

Configuration

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

Make a directory with your project name, for Salmon quantification. Configure the pipeline with cgatflow salmonquant config. A pipeline.log and pipeline.yml file(s) will be added to your new directory. Modify the pipeline.yml according to your project (specify genome, genome directory, annotation database and directory, database for uploading the outputs; specify options for Salmon quantification).

Pipeline use

Run the pipeline with cgatflow salmonquant make full.

For running the pipeline on a large set of samples, submit the pipeline onto the cluster (sharc), using a submit_pipeline_cgtaflow custom script.