Quick Start

The first step is to install RetroDetector and to ensure that you have all the necessary dependencies. Please see the Installation and Dependencies section for further information.

RetroDetector is built on the Snakemake workflow management system. The benefit of this is that Snakemake keeps track of all the steps in the pipeline and automatically takes care of resource management.

Any time you want to run RetroDetector to analyze the data for a new project, all you have to do is set up a new working directory, make a new configuration file with the locations of all the data files, and copy the Snakefile which has all the pipeline instructions.

So, make a working directory and change into that directory. For the rest of these instructions, please make sure you are in your working directory.

Now you can set up the configuration file according to your reference and sequencing files. Please see the Configuration section for further information.

Once you have set up the configuration file, you need to copy the Snakefile from your RetroDetector installation to your working directory. For example, if RetroDetector is installed at /user/software/RetroDetector you would run:

cp /user/software/RetroDetector/Snakefile .

Now you can finally run the RetroDetector pipeline. First, activate the snakemake environment and perform a dry run:

conda activate snakemake
snakemake -np

This should print to the console something like this:

this is a test

If there are no errors, then you can run RetroDetector. To run the pipeline, you have to tell RetroDetector how many cores you would like to use. For example, if you want to use 32 cores you would run:

snakemake --cores 32

RetroDetector will then map the sequencing reads to the transcriptome and genome and then identify any retrogenes. For more information about the pipeline, please see the RetroDetector Pipeline section. For more information about the final results produced by RetroDetector, please see the Results section.

If you want to see how to run RetroDetector on an example dataset, please see the Example Dataset section. For FAQs, please see the FAQs section. For advanced users, if you want information about adjusting advanced parameters in the pipeline, please see the Advanced Parameters section.

If you encounter any issues while running RetroDetector, please submit a GitHub issue here.