nekramer / CQTL_DE

Processing used for DE of CQTL project

CQTL_DE

The pipeline used for QC'ing and processing RNA-seq data for differential expression analysis in the CQTL project.

Workflow

1. Clone this entire repo into working directory:

   git clone https://github.com/nekramer/CQTL_DE.git

2. Edit the comma-separated samplesheet.csv to include sequencing samples of interest. The helper script makeSamplesheet.R was used for pulling various subsets of datasets from our internal sequencing samplesheets.

3. Edit config/config.yaml for parameters specific to analysis.

4. Submit workflow with sbatch:

   sbatch runRNAproc

To relaunch this workflow, unlock the directory with:

module load python/3.6.6
./unlock.sh RNAproc #or
./unlock.sh runRNAproc