Fastqc

Running Fastqc

We ran fastqc on all the reads in the Rawdata/Glycine_Max folder by submitting the job script to the HPC that can be seen below.  This job was run from within the  /share/bitcpt/S23/UnityID/Soy directory on the HPC.

job.sh parameters

The explanation for each of the components of the submission script can be found in the comment of the script below of each component. For example, the line #BSUB -n 20 requests 20 cores from the scheduler.

fastqc parameters

• /usr/local/usrapps/bitcpt/fastqc/bin/fastqc: The path to the fastqc program

• /share/bitcpt/S23/RawData/Glycine_max/*:The share file being used for the provided data

• -t 20: Run fastqc with 20 threads

• -outdir ./fastqc: Put the output of the fastqc run in a directory called fastqc that can be found in the current directory.

<Jobname>.sh script - Soybean

#BSUB -J fastqc_Soy #job name

#BSUB -n 20 #number of nodes

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

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

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

# For running fastqc on all my Soybean samples

# Run in working directory /share/bitcpt/S23/UnityID/Soy

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

# -t specifies number of threads

/usr/local/usrapps/bitcpt/fastqc/bin/fastqc /share/bitcpt/S23/RawData/Glycine_max/* -t 20 -outdir ./fastqc

FastQC output - Soybean

An html report will be generated for each .fq file in the glycine_max directory. An example is provided below that shows what this file will look like and contain. 

Saving fastqc files from the HPC

Perform this step using Globus files share and drag and drop files from the HPC to your personal computer.

List of fastqc soybean files with results