TrimGalore

Description

From the Trim Galore! Home Page: Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing).

Version

0.4.4

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

TrimGalore requires the following module file to run:

apps/trimgalore/0.4.4

See Modules for more information.

Running TrimGalore on CIRCE/SC

The TrimGalore user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

Note on CIRCE: Make sure to run your jobs from your $WORK directory!
Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

If, for example, you have wish to count the number of alignments in a BAM file, you would set up a submit script to use bamtools like this

#!/bin/bash
#
#SBATCH --job-name=trimgalore-test
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=output.%j.trimgalore_test

#### SLURM 1 processor trim_galore test to run for 2 hours.

# Load the trimgalore module:
module load apps/trimgalore/0.4.4

# Start trim_galore
trim_galore [options] <filename(s)>

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./trimgalore-test.sh

You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Trim Galore! Home Page:
- http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Trim Galore! User Guide:
- https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
- /apps/trimgalore/0.4.4/Docs

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with TrimGalore to the IT Help Desk: rc-help@usf.edu