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Pavlidis Lab RNA-seq pipeline repository

Python Package using Conda

This documentation is principally written to support the Pavlidis Lab, and we're still updating it. But this pipeline should be fairly easy to configure on any Linux servers using these instructions. External users interested in using this pipeline for RNA-Seq quantification should contact our helpdesk if troubleshooting assistance is needed.

Features

  • source mechanism that support discovery of samples from GEO, SRA, ArrayExpress and Gemma (in-house curation database)
  • built with STAR, RSEM, MultiQC, FastQC, and more
  • produces count and FPKM matrices suitable for analysis with R and Python
  • distributed via a workload manager thanks to Bioluigi
  • notify collaborators via Slack API
  • submit experiments defined in a Google Spreadsheet
  • web viewer to preview QC reports and download quantifications

Downloading and installing

Clone this repository:

git clone --recurse-submodules https://github.com/PavlidisLab/rnaseq-pipeline
cd rnaseq-pipeline

Note: We use a patched version of RSEM that honors the $TMPDIR environment variable for its intermediate outputs, fix issues with moving files across filesystems and uses STAR shared memory feature by default.

Create and activate a Conda environment with all the required software dependencies:

conda env create -f environment.yml
conda activate rnaseq-pipeline

Build the shared memory cleanup tool:

make -C scripts

Note: We remove unused shared memory objects allocated by STAR in Slurm task prolog and epilog scripts.

Build RSEM:

make -C contrib/RSEM

Install the pipeline Python package in the Conda environment:

pip install . # use -e if you want to edit the pipeline

Create a copy of the example.luigi.cfg file to luigi.cfg. It should work as-is, but you might want to change the output location and the resources.

First, you need to start Luigi scheduler daemon. You can see the progress of your tasks at http://localhost:8082/.

luigid

For convenience, we provide a luigi-wrapper script that sets the --module flag to rnaseq_pipeline.tasks for you.

luigi-wrapper <task> <task_args>

Setting up a genomic reference

The pipeline automatically generate the RSEM/STAR index and all that is required is to drop the GTF annotations file and the primary assembly FASTA files under pipeline-output/genome/<reference_id> subdirectory.

For example, you can setup a mouse reference from Ensembl by downloading the following files under pipeline-output/genomes/mm10_ensembl98:

  • ftp://ftp.ensembl.org/pub/release-98/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
  • ftp://ftp.ensembl.org/pub/release-98/gtf/mus_musculus/Mus_musculus.GRCm38.98.gtf.gz

Triggering tasks

The top-level task you will likely want to use is rnaseq_pipeline.tasks.GenerateReportForExperiment.

luigi-wrapper rnaseq_pipeline.tasks.GenerateReportForExperiment --source geo --taxon mouse --reference mm10_ensembl98 --experiment-id GSE80745

The output is organized as follow:

pipeline-output/
    genomes/<reference_id>/                 # Genomic references
    references/<reference_id>/              # RSEM/STAR indexes
    data/<source>                           # FASTQs (note that GEO source uses SRA)
    data-qc/<experiment_id>/<sample_id>/    # FastQC reports
    aligned/<reference_id>/<experiment_id>/ # alignments and quantification results
    quantified/<reference_id>               # quantification matrices for isoforms and genes
    report/<reference_id>/<experiment_id>/  # MultiQC reports for reads and alignments

You can adjust the pipeline output directory by setting OUTPUT_DIR under [rnaseq_pipeline] in the configuration.

[rnaseq_pipeline]
OUTPUT_DIR=/scratch/rnaseq-pipeline

Setting up distributed computation

The pipeline is build upon Bioluigi which supports dispatching external programs on a workload manager such as Slurm.

[bioluigi]
scheduler=slurm
scheduler_extra_args=[]

Web viewer

The pipeline comes with a Web viewer that provides convenient endpoints for consulting QC reports.

When installing, add the webviewer extra require which will include Flask and gunicorn:

pip install .[webviewer]
gunicorn rnaseq_pipeline.viewer:app

Gemma integration

The RNA-Seq pipeline is capable of communicating with Gemma using its RESTful API.

External spreadsheet via Google Sheets API

The RNA-Seq pipeline can pull experiment IDs from a collaborative spreadsheet through the Google Sheets API. This feature requires extra dependencies that are supplied by the gsheet extra require:

pip install .[gsheet]

The rnaseq_pipelines.tasks.SubmitExperimentsFromGoogleSpreadsheetToGemma task becomes available. We also have

submit-experiments-from-gsheet --spreadsheet-id <spreadsheet_id> --sheet-name <sheet_name>

The remote spreadsheet must be structured to have the following columns:

  • experiment_id, the Gemma exeriment short name
  • priority, the Luigi task priority, an integer
  • data, the status of the data, allowed values: ok, resubmit (forces a rerun), needs attention, all other values are ignored

Only experiments with strictly positive priority are scheduled.