Trinity On Terra

Terra

Instructions for running Trinity on Terra. The Trinity workflow is available here.

1. Upload your FASTQ files to your workspace bucket.

   Example:

   gsutil -m cp /foo/bar/projects/*.fastq.gz gs://my-bucket/
   

   Please see here for additional documentation.

2. Import CTAT/trinityrnaseq workflow to your workspace.

   See the Terra documentation for adding a workflow.

3. In your workspace, open trinityrnaseq in the WORKFLOWS tab. If you are running a single sample, select Run workflow with inputs defined by file paths, otherwise select Run workflow(s) with inputs defined by data table. Terra uses a workspace data table to run a workflow over multiple samples. Enter the workflow parameters and and click the Save button.

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Inputs

Please see the description of important inputs below.

Name	Description	Example Value
left	Array of left FASTQ files	["gs://my-bucket/10M.left.fq.gz"]
right	Array of right FASTQ files	["gs://my-bucket//10M.right.fq.gz"]
genome_guided_bam	BAM file for genome guided assembly	"gs://my-bucket//aligned.bam"
extra_args	Extra command line arguments to pass to Trinity	"--seqType fq --SS_lib_type RF"
memory_read_clustering_phase	Memory for read clustering phase (default 150G)	"25G"

Outputs

File	Description
Trinity.fasta	Trinity assembly FASTA
Trinity.fasta.gene_trans_map	File that maps gene to transcripts