Quick Links Documentation Interactive job Batch job Swarm of jobs

The weblogo package includes a tool ( seqlogo) to generate sequence logos from aligned sequences in fastq format.

Note that weblogo changed significantly from version 2.X to 3.X. The commands listed here are for versions 3.X

References

• G. E. Crooks, G. Hon, J. M. Chandonia, and S. E. Brenner. WebLogo: A sequence logo generator. Genome Research 2004, 14:1188-1190. Pubmed |  PMC |  Journal

Documentation

• Weblogo2

• Module Name: weblogo (see the modules page for more information)
• Singlethreaded
• Example files in $WEBLOGO_DATA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[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 weblogo
[+] Loading weblogo 3.6
[user@cn3144 ~]$ cp $WEBLOGO_DATA/* .
[user@cn3144 ~]$ weblogo -f ctcf.fa -F png -o ctcf.png

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

Visualization of the output image ctcf.png:

Create a batch script similar to the following example:

#! /bin/bash
#SBATCH --mem=100m
#SBATCH --time=5
# this file is seqlogo_job.sh

module load weblogo || exit 1
cp $WEBLOGO_DATA/* .
weblogo -f ctcf.fa -F png -o ctcf.png

Submit to the queue with sbatch:

biowulf$ sbatch seqlogo_job.sh

Create a swarm command file similar to the following example:

# this file is seqlogo_jobs.swarm
seqlogo -f site1.fa -F eps -o site1 -abcMnY
seqlogo -f site2.fa -F eps -o site2 -abcMnY
seqlogo -f site3.fa -F eps -o site3 -abcMnY
seqlogo -f site4.fa -F eps -o site4 -abcMnY

And submit to the queue with swarm

biowulf$ swarm -f seqlogo_jobs.swarm --time=5