Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

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)

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

[user@biowulf]$ sinteractive
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 seqfile1 .. seqfileN

Submit this job using the Slurm sbatch command.

sbatch --mem=10g 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 seqfile1 .. seqfileN
cd dir3;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
cd dir4;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
cd dir5;fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN

Submit this job using the swarm command.

swarm -f fastqc.swarm -g 10 --module fastqc

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module fastqc	Loads the fastqc module for each subjob in the swarm