RNA Seq Pipeline

A pipeline for basic RNA Seq analysis.

About this pipeline

This pipeline performs the introductory steps in any RNA Seq analysis:

• Trimming and aligning the reads for a sample.
• Counting the reads that align to various genomic features.

Important: This pipeline does not attempt any further analysis like DESeq or GSEA.

This pipeline is designed to run on a cluster environment, though some slight modification of the run script will cause it to run locally (see Running Locally).

Using this pipeline

This pipeline is built using metapipe. Before running, please run the setup script to fetch all of the required tools. If you don't want to use the setup sciript or you have different tools you'd like to use, you'll need to edit the metapipe file directly.

$ sh setup.sh path_to_bowtie_index path_to_gtf_file

Once the environment is set up, it's time to run the pipeline on your given samples.

To run the pipeline on a single sample, do the following:

$ sh run_one.sh <sample_id> <read_1_filename> <read_2_filename> 

To run a variety of samples, create a samples.txt file containing a line for each sample.

<sample_id> <read_1_filename> <read_2_filename>

Then run the following script.

$ sh run_all.sh samples.txt

Project Organization

This pipeline relies on a variety of external tools. Please make sure the paths are up to date for these tools.

Shortcut execution scripts are located on the top level and are the preferred way to execute the pipeline.

Running Locally

In order to run this pipeline locally, edit the pipeline.mp file and uncomment the paths to the local binaries. Then comment out or remove the cluster binary paths.

Note: The Trimmomatic settings has a path inbuilt which depends on the version you're using. You might have to change that if you're running it locally.