QC (Quality Control)

1. Log into the HPC

ssh lscapozi@login.hpc.ncsu.edu

2. Change the working directory to a login node

cd /share/bitcpt/Fall2022/lscapozi

3. Load conda and the required program

module load conda

conda init tcsh

4. Log out of Henry2 and log in again

exit

5. Change directory to Tom-Heinz1706

cd /share/bitcpt/Fall2022/lscapozi/Portfolio

6. Turn on conda software

module load conda

conda activate /usr/local/usrapps/bitcpt/fastqc

7. To check that fastqc has been successfully activated, you can print the fastqc help screen and also read useful options to use it right before employing it.

fastqc -h

8. Copy the fastqc script from Tom directory into Hz directory

cp /share/bitcpt/Fall2022/lscapozi/Tom/Tom.fastqc.sh .

9. Rename the fastqc script to fit the new Hz data

mv Tom.fastqc.sh Hz.fastqc.sh

10. Edit the fastqc script

vi Hz.fastqc.sh

#A new window will open up the the script

#Press "i" to edit

#Pres "Esc" followed by ":wq" to exit the script editing

#!/bin/tcsh

#BSUB -J fastqc_Hz_GroupName #job name

#BSUB -n 20 #number of nodes

#BSUB -W 2:0 #time for job to complete

#BSUB -o fastqc.out.%J #output file

#BSUB -e fastqc.err.%J #error file

# For running fastqc on all my Solanum_lycopersicum samples

# Run in working directory /share/bitcpt/Fall2022/lscapozi/Hz

# Must run this in working directory with subdirectory named /fastqc

module load conda

conda activate /usr/local/usrapps/bitcpt/fastqc

fastqc /share/bitcpt/Fall2022/RawData/Solanum_lycopersicum* -t 20 -outdir ./fastqc

11. Run the script

bsub <Hz.fastqc.sh

12. Check on job while it's running

bjobs