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
FastQC is developed by Simon Andrews, Babraham Bioinformatics.
Make sure X-windows is running while connecting to helix.
Sample session:
$ module load fastqc $ fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
First create a batch file alone the following lines:
#!/bin/bash
cd /data/$USER/mydir
module load fastqc
fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
Then submit this batch file to the cluster:
The default memory is 4 GB. Users may request more memory using the --mem flag:
Users may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.
biowulf$ sinteractive
salloc.exe: Granted job allocation 176863
[user@cnXXX]$ module load fastqc
[user@cnXXX]$ cd /data/$USER/fastqc/run1
[user@cnXXX]$ fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN
[user@cnXXX] exit
salloc.exe: Relinquishing job allocation 176863
salloc.exe: Job allocation 176863 has been revoked.
Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.
Set up a swarm command file (eg /data/username/cmdfile). Here is a sample file:
cd /data/user/somedir1; fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN cd /data/user/somedir2; fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN cd /data/user/somedir3; fastqc -o output_dir [-f fastq|bam|sam] -c contaminant_file seqfile1 .. seqfileN [...]
Submit this job with:
$ swarm -f cmdfile --module fastqc
By default, each line of the swarm command file will be executed on 1 core and 1.5 GB of memory. If you need more, then you should specify the required memory to swarm by using the -g # flag, where # is the number of GB of memory required. For example, if each command requires 10 GB of memory, submit with:
$ swarm -g 10 -f cmdfile --module fastqc
For more information regarding running swarm, see swarm.html
