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RNA-Seq – RSEM Simulation

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RNA-Seq – RSEM Simulation

In RNA-Seq, we can use simulated data, and this video shows how using the rsem-simulate-reads module.

In this tutorial we’ll be using the RNA-Seq function on the T-BioInfo platform.

We’ll be running a Simulation so we’ll be using RModelGenomeGTF, FastQ Data, single end pair reads and Arabidopsis Thaliana. Lets do a group of two, without comparison.

Now that we have our data input, lets make our pipeline. Firstly, we need to click start, and save the data we’ve input into the platform. We’re going to be using RSEM-simR today. There are a variety of options we can choose from but today we are just going to use the defaults.

Next, we’ll select bowtie-G, BS-exon, Bsklb-GPU, IsoLasso, cuffmerge and ROC curves. Finally we select data output.

To start our pipeline we need to click the cloud icon and then select ‘Run Pipeline’. Since this is a simulation, we don’t need to upload any data, it generates it’s own data.

The platform updates the page to show you your current pipeline and it’s progress. To see how it is progressing, you an either refresh the page or click on ‘My Pipelines’ at the top of the page. There is no need to sit and watch however, as the platform will email you when your pipeline is complete.

I hope you found this tutorial helpful, and thank you for your time.