Sam’s Notebook: Trimming/FastQC/MultiQC – C.bairdi RNAseq FastQ with fastp on Mox

After receiving our RNAseq data from Genewiz earlier today, needed to run FastQC, trim, check trimmed reads with FastQC.

FastQC on raw reads was run locally and files were kept on owl/nightingales/C_bairdi.

fastp trimming was run on Mox, followed by MultiQC.

FastQC on trimmed reads were run locally, followed by MultiQC.

SBATCH script (GitHub):

#!/bin/bash ## Job Name #SBATCH --job-name=cbai_fastp_trimming_RNAseq ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources ## Nodes #SBATCH --nodes=1 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=10-00:00:00 ## Memory per node #SBATCH --mem=120G ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=samwhite@uw.edu ## Specify the working directory for this job #SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20200318_cbai_RNAseq_fastp_trimming ### C.bairdi RNAseq trimming using fastp. # Exit script if any command fails set -e # Load Python Mox module for Python module availability module load intel-python3_2017 # Document programs in PATH (primarily for program version ID) { date echo "" echo "System PATH for $SLURM_JOB_ID" echo "" printf "%0.s-" {1..10} echo "${PATH}" | tr : \\n } >> system_path.log # Set number of CPUs to use threads=27 # Input/output files trimmed_checksums=trimmed_fastq_checksums.md5 raw_reads_dir=/gscratch/scrubbed/samwhite/data/C_bairdi/RNAseq/ # Paths to programs fastp=/gscratch/srlab/programs/fastp-0.20.0/fastp multiqc=/gscratch/srlab/programs/anaconda3/bin/multiqc ## Inititalize arrays fastq_array_R1=() fastq_array_R2=() programs_array=() R1_names_array=() R2_names_array=() # Programs array programs_array=("${fastp}" "${multiqc}") # Capture program options for program in "${!programs_array[@]}" do { echo "Program options for ${programs_array[program]}: " echo "" ${programs_array[program]} -h echo "" echo "" echo "