docs: better documentation of what the pipeline does

README.md

@@ -1,20 +1,27 @@
 # Snakemake pipeline for RNA-Seq analysis
 
+## Overview
+
 This pipeline runs the following steps:
 
 1. Download mouse reference genome, transcriptome and gene annotation files from [GENCODE](https://www.gencodegenes.org/mouse/).
 2. Run [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and [MultiQC](https://multiqc.info/) on the FASTQ files listed in the [design matrix](./config/design_matrix.csv).
 3. Use [Salmon](https://salmon.readthedocs.io/en/stable/salmon.html) to quantify transcript abundance for each sample.
-4. Use [STAR](https://github.com/alexdobin/STAR) to map reads to the genome into a BAM file, and count number of reads per gene while mapping. 
+4. Use [STAR](https://github.com/alexdobin/STAR) to map reads to the genome into a BAM file, and count number of reads per gene while mapping.
 5. Merge Salmon TPMs, Salmon read counts, and STAR read counts into three tables.
 6. Use [DESeq2](https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html) to compare transcript abundance between samples.
 
-To run this pipeline, install Snakemake following the [installation instructions](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html). Then after modifying the [configuration](./config/config.yml) file, run the pipeline with:
+## Getting started
+
+First install Snakemake following the official [installation instructions](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html). Next, modify the [configuration file](./config/config.yaml) to set the reference file versions and FASTQ file locations.
+
+Now we can simply run the pipeline with:
 
 ```bash
 snakemake -c <num-of-cores> --use-conda
 ```
 
+It's recommended to run the pipeline in `tmux` or `screen` as it can take a long time. Output to `stdout` are also saved to `.snakemake/log/`. Output of R scripts are saved to `logs/`.
 
 This pipeline will genrate the following subdirectories in the `results/` directory: