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Automated Execution of Trinotate: Running computes and loading results

Patrick Douglas edited this page Jul 11, 2018 · 2 revisions

Automated Execution of Trinotate: Running computes and loading results

Trinotate now comes with a script that automates the process of running all the above computes and loading the results. You’ll find it as:

$TRINOTATE_HOME/auto/autoTrinotate.pl
##############################################################################
#
# Required:
#
#  --Trinotate_sqlite <string>                Trinotate.sqlite boilerplate database
#
#  --transcripts <string>                     transcripts.fasta
#
#  --gene_to_trans_map <string>               gene-to-transcript mapping file
#
#  --conf <string>                            config file
#
#  --CPU <int>                                number of threads to use.
#
#
##############################################################################

The configuration file given to the --conf parameter describes the pipeline execution. An example config file is provided as:

$TRINOTATE_HOME/auto/conf.txt

Simply update the header portion of the conf.txt file to indicate the path to the programs you have installed and the paths to the resources indicated, and then run the script to process the data.

Trinotate: Sample data and execution

Sample data and a runMe.sh script are available at $TRINOTATE_HOME/sample_data/

Executing the runMe.sh script will pull down the Trinotate sqlite boilerplate database, populate with the provided bioinformatics computes, and generate the final Trinotate annotation report. In addition, pre-computed expression and DE analyses will be loaded for use with TrinotateWeb.

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