Folder on the cluster: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/matt_transcriptome/trim_galore
Trim_galore is a wrapper tool around Cutadapt and FastQC to apply quality and adapter trimming to FastQ files, with some extra functionality for RRBS-type libraries. I used Trim galore for adapter trimming and general quality filtering for paired-end RNASeq reads. I first ran FastQC on raw sequences and checked for adapter contamination. Once, I had an idea of the adapter sequences, I used Trim galore for the Illumina standard adapter trimming ('AGATCGGAAGAGC'). I used Trim_galore version 0.4.4. This version is installed globally on the UofU CHPC.
Softwares to loaded:
cutadapt locally installed in the trim_galore working directory
FastQC locally installed on UofU CHPC.
Here is a general command to run trim_galore on paired end reads:
trim_galore --fastqc --dont_gzip --paired read1.fastq read2.fastq
Here is gave the option --fastqc because I wanted the program to run fastqc after trimming. I gave the option --dont_gzip because I did not want the program to zip the output files.
Here is a bash script I used to run the program (change the file names and path as required):
#!/bin/bash #SBATCH -n 12 #SBATCH -N 1 #SBATCH -t 300:00:00 #SBATCH -p usubio-kp #SBATCH -A usubio-kp #SBATCH -J trimgalore module load cutadapt module load fastqc cd /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/matt_transcriptome/trim_galore/ /uufs/chpc.utah.edu/sys/pkg/trim_galore/trim_galore --fastqc --dont_gzip --paired ../rawdata/fastq/KS001_S71_L008_R1_001.fastq ../rawdata/fastq/KS001_S71_L008_R2_001.fastq ../rawdata/fastq/KS002_S72_L008_R1_001.fastq ../rawdata/fastq/KS002_S72_L008_R2_001.fastq ../rawdata/fastq/KS003_S73_L008_R1_001.fastq ../rawdata/fastq/KS003_S73_L008_R2_001.fastq ../rawdata/fastq/KS004_S74_L008_R1_001.fastq
../rawdata/fastq/KS004_S74_L008_R2_001.fastq ../rawdata/fastq/PMKS001_S109_L007_R1_001.fastq ../rawdata/fastq/PMKS001_S109_L007_R2_001.fastq ../rawdata/fastq/PMKS002_S110_L007_R1_001.fastq ../rawdata/fastq/PMKS002_S110_L007_R2_001.fastq ../rawdata/fastq/PMKS003_S111_L007_R1_001.fastq ../rawdata/fastq/PMKS003_S111_L007_R2_001.fastq ../rawdata/fastq/PMKS004_S112_L007_R1_001.fastq
../rawdata/fastq/PMKS004_S112_L007_R2_001.fastq ../rawdata/fastq/PMKS005_S113_L007_R1_001.fastq ../rawdata/fastq/PMKS005_S113_L007_R2_001.fastq ../rawdata/fastq/PMKS006_S114_L007_R1_001.fastq ../rawdata/fastq/PMKS006_S114_L007_R2_001.fastq ../rawdata/fastq/PMKS007_S115_L007_R1_001.fastq ../rawdata/fastq/PMKS007_S115_L007_R2_001.fastq ../rawdata/fastq/PMKS008_S116_L007_R1_001.fastq
../rawdata/fastq/PMKS008_S116_L007_R2_001.fastq