Trinity Example Files

Run Trinity in one step

This example runs all stages of Trinity in one step.   This is only advised for small datasets — datasets that require a maximum of 16 cores or 128 Gb of memory, and that are expected to completely finish within 96 hours. 

Files include:

  • trinity_all.job, PBS script     View it          Download
  • reads.left.fq.gz, input data    Download
  • reads.right.fq.gz, input data     Download
  • trinity_all.log, trinity output and error     Download
  • trinity_all.output, PBS standard output and error    Download

 

Run Trinity in multiple steps

Running Trinity in multiple steps is recommended for large datasets. If a job requires more than 96 hours to complete, PSC User Services can extend the time. To request a time extension, please contact User Services as soon as you know that it is necessary.

These jobs break the Trinity run into four steps:

  • Stage 1 - generate the kmer-catalog and runs Inchworm
  • Stage 2 - do the Chrysalis clustering of Inchworm contigs and mapping reads
  • Stage 3 - conduct the Chrysalis deBruijn graph construction
  • Stage 4 - run Butterfly and generate the final Trinity.fasta file

To run Trinity this way, submit the job for stage 1 (trinity_stage1.job). When it completes sucessfully, submit the second job, trinity_stage2.job, and so on.

Files include:

Stage 1: generate the kmer-catalog and run Inchworm

  • trinity_stage1.job, PBS script     View it          Download
  • reads.left.fq.gz, input data    Download
  • reads.right.fq.gz, input data     Download
  • trinity_stage1_example.log, trinity output and error     Download
  • trinity_stage1.output, PBS standard output and error    Download

Stage 2: do Chrysalis clustering of Inchworm contigs and mapping reads

  • trinity_stage2.job, PBS script     View it          Download
  • trinity_stage2_example.log, trinity output and error     Download
  • trinity_stage2.output, PBS standard output and error    Download

Stage 3: construct the Chrysalis deBruijn graphs

  • trinity_stage3.job, PBS script     View it          Download
  • trinity_stage3_example.log, trinity output and error     Download
  • trinity_stage3.output, PBS standard output and error    Download

Stage 4: run Butterfly and generate the final Trinity.fasta file

  • trinity_stage4.job, PBS script     View it         Download
  • trinity_stage4_example.log, trinity output and error     Download
  • trinity_stage4.output, PBS standard output and error    Download

Big Assemblies script

This script can be used for assemblies with more than 200 million reads or that use 64 or more cores. View It    Download

Last Updated on Thursday, 20 March 2014 10:15  

More on Trinity

Examples

  • Example files which show how to run Trinity in one run (for very small datasets) or in four stages (for larger datasets).

Documentation

User Information

PSC Passwords

Connect to PSC systems:

PSC Policies

For technical questions:
Call the PSC hotline: 412-268-6350 / 800-221-1641 or mail to remarks@psc.edu.

Other services PSC provides:

Advanced Networking: High-speed network design, testing and tuning

3ROX: High-speed network access

Biomedical Applications: Computational biomedical research and training