Fastq

FASTQC

FASTQC is a way to check the quality of the raw sequences obtained from high throughput sequencing methods, after the submitted job is completed a HTML file is produced; either as a base call file or color space file which can be imported to the personal computer through globus.org for interactive analysis.

The rawdata of Tomato Meristem and Leaf sequences are checked for quality, a green check on each of the categories (image to the left) indicates good quality.

Script Below:

#!/bin/tcsh

#BSUB -J fastqc_Tom_GroupName #job name

#BSUB -n 20 #number of nodes (number of nodes requested for the job)

#BSUB -W 2:0 #time for job to complete (wall clock time after which the job will be automatically deleted)

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

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

# For running fastqc on all my Solanum samples

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

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

module load conda (initiates conda)

conda activate /usr/local/usrapps/bitcpt/fastqc (path to FASTQC software)

# -t specifies number of threads

fastqc /share/bitcpt/Fall2022/RawData/Solanum_lycopersicum/* -t 20 -o ./fastqc (path to number of threads to use and output directory)

Page updated

Report abuse