RNAseq-upstream

Workflow to generate count table from paired-read RNA-seq.

Prerequisites

The main workflow uses the following software/packages:

1. QC, adapter and quality trimming - Fastp
2. Alignment and Count - STAR

It's recommended to install the softwares with conda:

1. Create conda environment: conda create -n rna-seq
2. Configure package channels:
   conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
   For Apple Silicon Mac, additionally run conda config --add subdirs osx-64
3. Install packages:
   conda install -n rna-seq -c bioconda star fastp

Run the workflow

It's recommended to run this workflow on a High-Performance Computing Server (For example, CRC machines)