Trans-ABySS

Description

From the Trans-ABySS web site: Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. The pipeline accepts assemblies that were generated across a wide range of k values in order to address variable transcript expression levels. It first filters and merges the multi-k assemblies, generating a much smaller set of nonredundant contigs. It contains scripts that map assembled contigs to known transcripts, currently supporting the Blat contig-to-genome aligner. It identifies novel splicing events like exon-skipping, novel exons, retained introns, novel introns, and alternative splicing. Its scripts can also identify candidate gene-fusions, single-nucleotide variants, insertions, deletions, and inversions.

• Trans-ABySS Home Page

Version

• 1.4.4

Authorized Users

• CIRCE account holders

Platforms

• CIRCE cluster

Running Trans-ABySS Jobs on CIRCE

Modules

Before running a job, you must first set up your environment properly. Here are the required module files:

• apps/trans-abyss/1.4.4

To run Trans-ABySS on the cluster, ensure that you use module add prior to using any executables. See Modules for more information.

How to Submit Jobs

Provided is a batch script for running Trans-ABySS executables on the cluster. This script can be copied into your work directory (the folder with your input files and database files) so that you can submit batch processes to the queue.
Then, change the “Submit the Job” section to:

If, for example, you have a Trans-ABySS input file named trans-abyss.in, you would set up a submit script like this:

• The script below (for testing, name it “trans-abyss-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our SLURM User’s Guide. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.

#!/bin/bash
#
#SBATCH --comment=trans-abyss-test
#SBATCH --ntasks=4
#SBATCH --job-name=trans-abyss-test
#SBATCH --output=output.%j.trans-abyss-test
#SBATCH --time=01:00:00

#### Slurm 4 processor Trans-ABySS test to run for 1 hour.

module purge
module load apps/trans-abyss/1.4.4

python wrappers/trans_abyss.py  

 
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 ./trans-abyss-test.sh

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

Additional Documentation

• Trans-ABySS Manual
  • /apps/trans-abyss/1.4.4/trans-abyss-manual-v1.4.4.pdf

• Trans-ABySS User's Guide
  • http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss/releases/1.4.4

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

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