Oases

Description

From the Oases home page: Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. Oases uploads a preliminary assembly produced by Velvet, and clusters the contigs into small groups, called “loci”. It then exploits the paired-end read and long read information, when available, to construct transcript isoforms.

Version

  • 0.1.22

Authorized Users

  • CIRCE account holders
  • RRA account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • RRA cluster
  • SC cluster

Modules

Oases requires the following module file to run:

  • apps/oases/0.1.22

Running Oases on CIRCE/SC

The Oases 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 Oases 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.

Serial Submit Script

You must first process the reads using Velvet:

  • you must choose a hash length at this stage (cf. the Velvet manual),
  • DO NOT set a coverage cutoff, you should set that when running oases,
  • DO NOT set an expected coverage,
  • remember to turn on the -read_trkg option when running velvetg.

You can run Oases on your data working directory after it has been created and processed by Velvet. Provide all the information about insert lengths and their standard deviation as possible (identical to Velvet)

An example of processing in velvet (using “test_reads.fa” from the known tests directory listed below) is: 

[johndoe@login1 ~]$ mkdir /work/j/johndoe/oases
[johndoe@login1 ~]$ mkdir /work/j/johndoe/oases/data
[johndoe@login1 ~]$ cd /work/j/johndoe/oases
[johndoe@login1 mega]$ cp /opt/apps/oases/0.1.22/data/test_reads.a /work/j/johndoe/oases/data
[johndoe@login1 mega]$ velveth /work/j/johndoe/oases/data 21 -shortPaired /work/j/johndoe/oases/data/test_reads.fa
[johndoe@login1 mega]$ velvetg /work/j/johndoe/oases/data/ -read_trkg yes
[johndoe@login1 mega]$

You will then be ready to process the data directory with Oases.

If, for example, you wrote your velveth/velvetg output to $WORK/oases/data, you would set up a submit script like this:

  • The script below (for testing, name it “oases-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=oases-test
#SBATCH --ntasks=4
#SBATCH --job-name=oases-test
#SBATCH --output=output.%j.oases-test
#SBATCH --time=01:00:00

#### SLURM 4 processor Oases test to run for 1 hour.

module add apps/oases/0.1.22
oases $WORK/data -ins_length 200

 
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 ./oases-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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

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