RNA-seq Pipeline Comparison and Analyses

A Snakemake workflow for running TALON, FLAIR, and pipeline-nanopore-ref-isoforms. Performs a comparative analyses of results using tools such as GFFcompare.

Flowchart

Dependencies

1. Snakemake 7.3.1
   A full snakemake instalation is recommended
2. Singularity 3.7.0

Installation

Clone the repository to desired location.

How to run

1. Set parameters in config.yaml
2. run: snakemake -p --use-singularity --singularity-prefix "resources" --singularity-args "--bind *" --use-conda -j ** all --configfile "config/config.yaml"

Note * : You should provide your own directory for the --bind command so that the data is accesible from the singularity containers.
Note ** : Specify number of available threads here.

Snakemake report

You can run snakemake --report report.html AFTER the workflow finished to create a report containing results.

Notes

The GTF files located in the 03_combined and 05_matched_transcripts have a column called TPM. This is not the Actual TPM value but the raw number of counts. The atrribute is hijacked to pass counts to GFFCompare.

Troubleshooting

Transcriptclean

Transcriptclean requires the reference genome fasta file to only have one string per header.

Conda environment fails to build

Try running the workflow with an older version of snakemake such as version 5.3.2.

License

MIT, see LICENSE