brucemoran / rdl_rnaseq

BD Han2 Rat Model of Endometrial Cancer

Analysis of Endometrial Carcinoma in BD Han II Rats

Dependencies

The repo contains NextFlow pipelines run inside Singularity containers.

This is relatively easily set up following respective installation instructions through the links.

Steps to Reproduce Analysis

1: Clone repo into desired location

github clone https://github.com/brucemoran/rdl_RNAseq && cd rdl_RNAseq

2: Run RNAseq_STAR-kallisto_references.simg.nf to generate reference data

nextflow run refs.nf \
          --outDir "refs" \
          --set "rat" \
          -profile standard,refs

3: Download sample data and generate sampleCsv input

4: Run RNAseq_STAR-kallisto.simg.nf to generate output

nextflow run main.nf \
          --sampleCsv "data/sample.csv" \
          --projectBase "./" \
          --refsDir "refs" \
          --noStar \
          -profile standard