FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

The main functions of FastQC are

- Import of data from BAM, SAM or FastQ files (any variant)
- Providing a quick overview to tell you in which areas there may be problems
- Summary graphs and tables to quickly assess your data
- Export of results to an HTML based permanent report
- Offline operation to allow automated generation of reports without running the interactive application

References:

• FastQC is developed by Simon Andrews, Babraham Bioinformatics.

• http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

• Module Name: fastqc (see the modules page for more information)
• For bulk jobs, please allocated lscratch so that the temporary files could be storaged at local disk instead of working directory. It is more efficient for your job and for the system as a whole if you use local disk. See the examples and read more on using local disk in the Biowulf User Guide.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --lscratch=10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load fastqc
[user@cn3144 ~]$ fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. fastqc.sh). For example:

#!/bin/bash
set -e
module load fastqc
fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file -t $SLURM_CPUS_PER_TASK seqfile1 .. seqfileN 

Submit this job using the Slurm sbatch command.

sbatch --mem=10g -c 4 --gres=lscratch:20 fastqc.sh

Create a swarmfile (e.g. fastqc.swarm). For example:

cd dir1;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
cd dir2;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile2
cd dir3;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile3
cd dir4;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile4
cd dir5;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile5

Submit this job using the swarm command.

swarm -f fastqc.swarm -g 10 --gres=lscratch:20 --module fastqc