02. FastQC to check the quality of the raw reads

#!/bin/bash

#SBATCH -n 12                   # use all 32 cores on the SMP node
#SBATCH -p private
#SBATCH --job-name=fastQC_catTrim_KH11_KH15
#SBATCH -t 0-2:0                # time 
#SBATCH -A mwilsons
#SBATCH -o slurm.fastQC_catTrim_KH11_KH15.out
#SBATCH -e slurm.fastQC_catTrim_KH11_KH15.err  
#SBATCH --mail-type=END,FAIL 
##SBATCH --mail-user=kcolney@asu.edu # 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/catlane_fastq

#--------------------------
# 3. load module 
#--------------------------

module load fastqc/0.11.3 

#--------------------------
# 4. fastqc
#--------------------------

#parallel -j10 fastqc *{1}Trim*.fastq::: KH11_ KH12_ KH13_ KH14_ KH15_ 

fastqc KH11_Trim_430minlen50.fastq
fastqc KH12_Trim_430minlen50.fastq
fastqc KH13_Trim_430minlen50.fastq
fastqc KH14_Trim_430minlen50.fastq
fastqc KH15_Trim_430minlen50.fastq


 
#--------------------------
# 5. end timer
#--------------------------

date