RNAseq

Trimming to featurecounts snakemake

Currently Loaded Modules:

module load gbc-samtools/1.12 gbc-hisat2/2.2.1 gbc-cutadapt/1.16 python/py37-anaconda-2019.10 snakemake/5.7.1-py37 gbc-fastqc gbc-subread

Step-by-step of install and analysis

1. git clone this repository

git clone https://github.com/achisha21/RNAseq-snakemake.git

2. Activate the python anaconda environment

conda activate snakemake

3. Edit the config.json file and cluster.json files

4. Ensure meta-data table contains all of the necessairy fields

** NOTE EXACT HEADERS HAVE TO BE ENFORCED or key errors will be thrown during processing**

5. Launch jobs The use of --latency-wait allows for SLURM to catch up writing the files and posting the file handles so Snakemake can see them.

snakemake --latency-wait 120 -p -j 100 --profile slurm

6. Pipeline should result in a featurecount file