Running tRNAnalysis - Tutorial¶
Before beginning this tutorial make sure you have tRNAnalysis installed correctly, please see here (see Installation) for installation instructions.
In the following section we will run a toy example pipeline that demonstrates the functionality of tRNAnalysis. tRNAnalysis can be run locally or distributed across a cluster. This tutorial will explain the steps required to run tRNAnalysis.
1. First download the tutorial data:
wget https://www.cgat.org/downloads/public/adam/trnanalysis/test_trna.tar.gz tar -zxvf test_trna.tar.gz
2. Next we will generate a configuration yml file so the pipeline output can be modified:
cd test_trna trnanalysis config
This will generate a pipeline.yml file containing the configuration parameters than can be used to modify the output of the pipeline. These parameters can all be modified to change the output or running of tRNAnalysis. However, for this tutorial you do not need to modify the parameters to run the pipeline as the default ones are appropriate in this instance.
There is already a pipeline.yml file within the test data so you don’t really need to run the command above this time.
3. Next we will run the pipeline:
trnanalysis make full -v5 --no-cluster
--no-cluster will run the pipeline locally if you do not have access to a cluster. Alternatively if you have a
cluster remove the
--no-cluster option and the pipeline will distribute your jobs across the cluster.
For information on how to configure your cluster please see the
cluster config help.
There are many commandline options available to run the pipeline. To see available options please run
The pipeline is mostly quite quick to execute. However, it can take a considerable time to generate the bowtie indexes, in the future we will parameterise this so you can use pre-configured bowtie indexes so these do not have to keep being generated each time the pipeline is ran.
4. Generate a report
The final step is to generate a report to display the output of tRNAnalysis. The tutorial contains all of the files already set up for you to run the report without the need to modify any of them. However, we recommend that you look at the The tRNAnalysis report for how to set up the clustering and differential expression correctly.
The report is generated by running the command:
trnanalysis make build_report -v 5 --no-cluster
This will generate a MultiQC report in the folder MultiQC_report.dir/ and an Rmarkdown report in R_report.dir/Final_report/index.html.
However, you can access the report by double clicking the FinalReport.html file within the directory that tRNAnalysis was executed.
This completes the tutorial for running the tRNAnalysis , hope you find it as useful as we do for analysing tRNA sequencing data.