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 generates the kmer-catalog and runs Inchworm
- Stage 2 does the Chrysalis clustering of Inchworm contigs and mapping reads
- Stage 3 conducts the Chrysalis deBruijn graph construction
- Stage 4 Runs Butterfly and generates 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
