FastQC

Login

1. Login into HPC

mcescalo@login.hpc.ncsu.edu

2. Change the working directory to my user name under bitcpt group

>>: cd /share/bitcpt/Fall2022/mcescalo/Portafolio

QUALITY CONTROL USING FASTQC

1. Create a new Sunflower working directory and subdirectories for Tomato RNAseq project

mkdir Tom

### You should be in "/share/bitcpt/Spring2022/mcescalo working directory

2. Change working directory to "Tom"

cd /Tom

3. create sub-directories in Tom directory

mkdir AlignedToTranscriptome fastqc salmon_align_quant starindices starOutputfiles transcriptome

4. List out the subdirectories and files inside Ha directory using tree command

tree

├── AlignedToTranscriptome

├── fastqc

├── salmon_align_quant

├── starindices

├── starOutputfiles

└── transcriptome

5. Create "Toma.fastqc.sh" shell script

vi Toma.fastqc.sh

#!/bin/tcsh

#BSUB -J fastqc_At_Genes #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 Tomato samples

# Run in working directory /share/bitcpt/Fall2022/mcescalo/Tom

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

module load conda

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

# -t specifies number of threads

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

6. Submit the job to run the FastQC

bsub < Toma.fastqc.sh

7. After successful job completion, change the working directory to "fastqc" subdirectory

cd /fastqc

8. List out all the files generated by the FastQC scripts using "tree" command

tree

.

├── Sl_Leaf_Rep1_1_fastqc.html

├── Sl_Leaf_Rep1_1_fastqc.zip

├── Sl_Leaf_Rep1_2_fastqc.html

├── Sl_Leaf_Rep1_2_fastqc.zip

├── Sl_Leaf_Rep1_2X_1_fastqc.html

├── Sl_Leaf_Rep1_2X_1_fastqc.zip

├── Sl_Leaf_Rep1_2X_2_fastqc.html

├── Sl_Leaf_Rep1_2X_2_fastqc.zip

├── Sl_Leaf_Rep1_3X_1_fastqc.html

├── Sl_Leaf_Rep1_3X_1_fastqc.zip

├── Sl_Leaf_Rep1_3X_2_fastqc.html

├── Sl_Leaf_Rep1_3X_2_fastqc.zip

├── Sl_Leaf_Rep2_1_fastqc.html

├── Sl_Leaf_Rep2_1_fastqc.zip

├── Sl_Leaf_Rep2_2_fastqc.html

├── Sl_Leaf_Rep2_2_fastqc.zip

├── Sl_Leaf_Rep2_2X_1_fastqc.html

├── Sl_Leaf_Rep2_2X_1_fastqc.zip

├── Sl_Leaf_Rep2_2X_2_fastqc.html

├── Sl_Leaf_Rep2_2X_2_fastqc.zip

├── Sl_Leaf_Rep2_3X_1_fastqc.html

├── Sl_Leaf_Rep2_3X_1_fastqc.zip

├── Sl_Leaf_Rep2_3X_2_fastqc.html

├── Sl_Leaf_Rep2_3X_2_fastqc.zip

├── Sl_Leaf_Rep3_1_fastqc.html

├── Sl_Leaf_Rep3_1_fastqc.zip

├── Sl_Leaf_Rep3_2_fastqc.html

├── Sl_Leaf_Rep3_2_fastqc.zip

├── Sl_Leaf_Rep3_2X_1_fastqc.html

├── Sl_Leaf_Rep3_2X_1_fastqc.zip

├── Sl_Leaf_Rep3_2X_2_fastqc.html

├── Sl_Leaf_Rep3_2X_2_fastqc.zip

├── Sl_Leaf_Rep3_3X_1_fastqc.html

├── Sl_Leaf_Rep3_3X_1_fastqc.zip

├── Sl_Leaf_Rep3_3X_2_fastqc.html

├── Sl_Leaf_Rep3_3X_2_fastqc.zip

├── Sl_SAM_Rep1_1_fastqc.html

├── Sl_SAM_Rep1_1_fastqc.zip

├── Sl_SAM_Rep1_2_fastqc.html

├── Sl_SAM_Rep1_2_fastqc.zip

├── Sl_SAM_Rep1_2X_1_fastqc.html

├── Sl_SAM_Rep1_2X_1_fastqc.zip

├── Sl_SAM_Rep1_2X_2_fastqc.html

├── Sl_SAM_Rep1_2X_2_fastqc.zip

├── Sl_SAM_Rep1_3X_1_fastqc.html

├── Sl_SAM_Rep1_3X_1_fastqc.zip

├── Sl_SAM_Rep1_3X_2_fastqc.html

├── Sl_SAM_Rep1_3X_2_fastqc.zip

├── Sl_SAM_Rep2_1_fastqc.html

├── Sl_SAM_Rep2_1_fastqc.zip

├── Sl_SAM_Rep2_2_fastqc.html

├── Sl_SAM_Rep2_2_fastqc.zip

├── Sl_SAM_Rep2_2X_1_fastqc.html

├── Sl_SAM_Rep2_2X_1_fastqc.zip

├── Sl_SAM_Rep2_2X_2_fastqc.html

├── Sl_SAM_Rep2_2X_2_fastqc.zip

├── Sl_SAM_Rep2_3X_1_fastqc.html

├── Sl_SAM_Rep2_3X_1_fastqc.zip

├── Sl_SAM_Rep2_3X_2_fastqc.html

├── Sl_SAM_Rep2_3X_2_fastqc.zip

├── Sl_SAM_Rep3_1_fastqc.html

├── Sl_SAM_Rep3_1_fastqc.zip

├── Sl_SAM_Rep3_2_fastqc.html

├── Sl_SAM_Rep3_2_fastqc.zip

├── Sl_SAM_Rep3_2X_1_fastqc.html

├── Sl_SAM_Rep3_2X_1_fastqc.zip

├── Sl_SAM_Rep3_2X_2_fastqc.html

├── Sl_SAM_Rep3_2X_2_fastqc.zip

├── Sl_SAM_Rep3_3X_1_fastqc.html

├── Sl_SAM_Rep3_3X_1_fastqc.zip

├── Sl_SAM_Rep3_3X_2_fastqc.html

├── Sl_SAM_Rep3_3X_2_fastqc.zip

├── Sl_SAM_Rep4_1_fastqc.html

├── Sl_SAM_Rep4_1_fastqc.zip

├── Sl_SAM_Rep4_2_fastqc.html

├── Sl_SAM_Rep4_2_fastqc.zip

├── Sl_SAM_Rep4_2X_1_fastqc.html

├── Sl_SAM_Rep4_2X_1_fastqc.zip

├── Sl_SAM_Rep4_2X_2_fastqc.html

├── Sl_SAM_Rep4_2X_2_fastqc.zip

├── Sl_SAM_Rep4_3X_1_fastqc.html

├── Sl_SAM_Rep4_3X_1_fastqc.zip

├── Sl_SAM_Rep4_3X_2_fastqc.html

└── Sl_SAM_Rep4_3X_2_fastqc.zip

0 directories, 84 files