tsrna-de

A Nextflow pipeline for the identification, quantification and analysis of tRNA fragments in small/miRNA-seq datasets

Basis

• Analyse all FASTQs
• trim and QC
• align reads using STAR
• collapse SAM multi-mappers
• count features
• collate using MultiQC

Quickstart

Comparing two conditions (e.g. control vs treatment)

git clone https://github.com/GiantSpaceRobot/tsrna-de.git
nextflow run tsrna-de --species mouse --input_dir tsrna-de/ExampleData/ --layout tsrna-de/additional-files/Example_ExperimentLayout.csv --output_dir My_Results

On finishing the run, the pipeline will generate PDFs and CSVs in the specified output directory

More Information

tsrna-de steps and parameters

Steps:

• Execute tsrna-de
  1. FASTQC
  2. MULTIQC
  3. trim_galore
  4. STAR
  5. Collapse SAM files
  6. tRNA counts (using featureCounts)
  7. tsRNA counts (using SAM-to-tsRNAcount.py script in bin)
  8. Run DESeq2 on tsRNA counts

Parameters:

• Run the following for a breakdown of parameters: nextflow run tsrna-de --help

Contributors

• Paul Donovan, PhD

License

This project is licensed under the MIT License.