Nextflow-RNASEQ

This is a project for RNA Sequence Analysis using Nextflow pipeline.

Environment Setup

• install nextflow

  cd ~
  wget -qO- https://get.nextflow.io | bash
  chmod +x nextflow

  • You can move the executable nextflow to /usr/bin/ to directly use it
  • Nextflow on ErisOne: /data/bioinformatics/tools/nextflow_new
    • The /data/bioinformatics/tools/nextflow is old one, please delete it and rename the nextflow_new when anyone is permitted

• Dependencies

  • conda
  • rMATS
    • On ErisOne: /data/bioinformatics/tools/run_rmats
  • TO BE TEST ON ERISONE
    • bioinformatics tools like fastqc, trim_galorestar
    • python packages

Pipeline Confioguratio

• For basic configuration, reference to ./conf/sample.config or ./conf/test.config

  • input/output path
  • genome type
    • preconfigured genomes saved in ./conf/igenomes.config
    • you can choose genome type from ./conf/igenomes.config
    • you can also provide STAR Index, gtf by your self

• For advanced configuration, reference to ./nextflow.config

  • like parameters for each algorithm or tool
  • check the parameters in the file
  • config them in ./conf/YOUR_SAMPLE_NAME.config
  • you can reference to ./conf/sample.config -> STAR Options