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03. Trim fastq files for quality
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03. Trim fastq files for quality
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#!/bin/bash
#SBATCH -n 8 # use all 32 cores on the SMP node
##SBATCH -p private
#SBATCH --job-name=Trim_FASTQC_eachlane
#SBATCH -t 0-8:0 # time
#SBATCH -A mwilsons
#SBATCH -o slurm.Trim_FASTQC_eachlane.out
#SBATCH -e slurm.Trim_FASTQC_eachlane.err
#SBATCH --mail-type=END,FAIL
#SBATCH [email protected] # If you want it to email you when the job is completed or fails
################################
# Trimmming
#--------------------------
# 1. start timer
#--------------------------
date
#--------------------------
# 2. move to the appropriate directory
#--------------------------
cd /home/kcolney/cancer_HaynesLab/raw_fastq
#--------------------------
# 3. load module
#--------------------------
module load fastqc/0.11.3
module load java/latest
#--------------------------
# 4. trim the fastq files for each of the 4 lanes for each sample
#--------------------------
# trim the fastq files
parallel -j20 java -jar /home/kcolney/ngcchome/tools2/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 {1}_L001_R1_001.fastq /home/kcolney/cancer_HaynesLab/trim_eachlane/{1}_L001_Trim_430minlen50.fastq ILLUMINACLIP:/home/kcolney/ngcchome/tools2/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:10 TRAILING:25 SLIDINGWINDOW:4:30 MINLEN:50 ::: KH1_S1 KH2_S2 KH3_S3 KH4_S4 KH5_S5 KH6_S6 KH7_S7 KH8_S8 KH9_S1 KH10_S2 KH11_S3 KH12_S4
parallel -j20 java -jar /home/kcolney/ngcchome/tools2/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 {1}_L002_R1_001.fastq /home/kcolney/cancer_HaynesLab/trim_eachlane/{1}_L002_Trim_430minlen50.fastq ILLUMINACLIP:/home/kcolney/ngcchome/tools2/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:10 TRAILING:25 SLIDINGWINDOW:4:30 MINLEN:50 ::: KH1_S1 KH2_S2 KH3_S3 KH4_S4 KH5_S5 KH6_S6 KH7_S7 KH8_S8 KH9_S1 KH10_S2 KH11_S3 KH12_S4
parallel -j20 java -jar /home/kcolney/ngcchome/tools2/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 {1}_L003_R1_001.fastq /home/kcolney/cancer_HaynesLab/trim_eachlane/{1}_L003_Trim_430minlen50.fastq ILLUMINACLIP:/home/kcolney/ngcchome/tools2/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:10 TRAILING:25 SLIDINGWINDOW:4:30 MINLEN:50 ::: KH1_S1 KH2_S2 KH3_S3 KH4_S4 KH5_S5 KH6_S6 KH7_S7 KH8_S8 KH9_S1 KH10_S2 KH11_S3 KH12_S4
parallel -j20 java -jar /home/kcolney/ngcchome/tools2/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 {1}_L004_R1_001.fastq /home/kcolney/cancer_HaynesLab/trim_eachlane/{1}_L004_Trim_430minlen50.fastq ILLUMINACLIP:/home/kcolney/ngcchome/tools2/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:10 TRAILING:25 SLIDINGWINDOW:4:30 MINLEN:50 ::: KH1_S1 KH2_S2 KH3_S3 KH4_S4 KH5_S5 KH6_S6 KH7_S7 KH8_S8 KH9_S1 KH10_S2 KH11_S3 KH12_S4
parallel -j20 java -jar /home/kcolney/ngcchome/tools2/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 {1}_L001_R1_001.fastq /home/kcolney/cancer_HaynesLab/trim_eachlane/{1}_L001_Trim_430minlen50.fastq ILLUMINACLIP:/home/kcolney/ngcchome/tools2/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:10 TRAILING:25 SLIDINGWINDOW:4:30 MINLEN:50 ::: KH13_S5 KH14_S6 KH15_S7 KH16_S8 KH17_S9 KH18_S9 KH19_S10 KH20_S10 KH21_S11 KH22_S11 KH23_S12 KH24_S12
parallel -j20 java -jar /home/kcolney/ngcchome/tools2/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 {1}_L002_R1_001.fastq /home/kcolney/cancer_HaynesLab/trim_eachlane/{1}_L002_Trim_430minlen50.fastq ILLUMINACLIP:/home/kcolney/ngcchome/tools2/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:10 TRAILING:25 SLIDINGWINDOW:4:30 MINLEN:50 ::: KH13_S5 KH14_S6 KH15_S7 KH16_S8 KH17_S9 KH18_S9 KH19_S10 KH20_S10 KH21_S11 KH22_S11 KH23_S12 KH24_S12
parallel -j20 java -jar /home/kcolney/ngcchome/tools2/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 {1}_L003_R1_001.fastq /home/kcolney/cancer_HaynesLab/trim_eachlane/{1}_L003_Trim_430minlen50.fastq ILLUMINACLIP:/home/kcolney/ngcchome/tools2/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:10 TRAILING:25 SLIDINGWINDOW:4:30 MINLEN:50 ::: KH13_S5 KH14_S6 KH15_S7 KH16_S8 KH17_S9 KH18_S9 KH19_S10 KH20_S10 KH21_S11 KH22_S11 KH23_S12 KH24_S12
parallel -j20 java -jar /home/kcolney/ngcchome/tools2/Trimmomatic-0.36/trimmomatic-0.36.jar SE -phred33 {1}_L004_R1_001.fastq /home/kcolney/cancer_HaynesLab/trim_eachlane/{1}_L004_Trim_430minlen50.fastq ILLUMINACLIP:/home/kcolney/ngcchome/tools2/Trimmomatic-0.36/adapters/TruSeq3-PE.fa:2:30:10 LEADING:10 TRAILING:25 SLIDINGWINDOW:4:30 MINLEN:50 ::: KH13_S5 KH14_S6 KH15_S7 KH16_S8 KH17_S9 KH18_S9 KH19_S10 KH20_S10 KH21_S11 KH22_S11 KH23_S12 KH24_S12
#--------------------------
# 5. end timer
#--------------------------
date