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.

Version

  • 1.4.4

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Trans-ABySS requires the following module file to run:

  • apps/trans-abyss/1.4.4

Running Trans-ABySS on CIRCE/SC

The Trans-ABySS 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.

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.
#!/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

Documentation

Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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