RNAseq in Open Mind

This needs to have an account in OpenMind

  1. Open the terminal

  2. ssh username@openmind7.mit.edu

  3. cd /om/user/username

  4. mkdir rnaseq-pilm211

  5. cd rnaseq-pilm211

  6. ls /om/group/pilm/test_data/mouse

  7. cp /om2/group/pilm/master-scripts/pipelines-nf-rnaseq/* . and cp /om2/group/pilm/master-scripts/config/om-profile.config .

  8. vim om-job.slurm

modify the line to look like this: (remove the # character to uncomment the line and it actually runs)

#!/bin/bash
#SBATCH -N 1
#SBATCH -c 1
#SBATCH --mem=4000
#SBATCH -t 0-23:00:00
#SBATCH -J "rnaseq"
#SBATCH -e job.e
#SBATCH -o job.o
## SBATCH --mail-type=END,FAIL # this line is commented
## SBATCH --mail-user=user@mit.edu  # this line is commented

export PATH=/om2/group/pilm/conda3/envs/nf-core-rnaseq-1.4dev/bin:$PATH
export PATH=/om2/group/pilm/bin:$PATH

if [ ! -f "om-profile.config" ] ; then
  cp  /om2/group/pilm/master-scripts/config/om-profile.config .
fi
if [ ! -f "om-rnaseq" ] ; then
  cp  /om2/group/pilm/master-scripts/pipelines-nf-rnaseq/om-rnaseq.config .
fi

## Example pipeline
GENOME=/om/group/pilm/genomes/Mmusculus/GRCm38.96/GRCm38.96.config
#GENOME=/om/group/pilm/genomes/Mmusculus/GRCh38.96/GRCh38.96.config

# Add --singleEnd if true
nextflow run /om2/group/pilm/pipelines/dev/pipelines-nf-rnaseq -c om-profile.config -c om-rnaseq.config -c $GENOME  --reads "/om/group/pilm/test_data/mouse/*_{1,2}.fastq.gz" -resume

Default parameters

The PILM pipeline runs under some default parameters in the following files.

General

om-profile.config

executor {
  queueSize=24
}

process {

  // Global process config
  executor = 'slurm'
  // queue = ''
  cpus = 6
  // clusterOptions = { "--qos=" }

}
  • queueSize is the number of jobs running at the same time.
  • cpus the number of cores by default to use by process

RNAseq

om-rnaseq.config

params {
  igenomes_base = '/om/group/pilm/genomes'
  skipRseQC = true
  skipGenebodyCoverage = true
  skipPreseq = true
  skipDupRadar = true
  aligner = 'hisat2'
  pseudo_aligner = 'salmon'
}