Projects and Tutorials

Big Data Analysis NGS Data RNA-seq
Grosmannia clavigera
Document Video

RNA-Seq Analysis Tutorial – Grosmannia clavigera

User Ratings :

After following the steps in the above video, the files used for uploading sample and genome data are referenced by the SVL files contained in this zip: click here to download it.

Those steps include:

When visiting the front page of T-BioInfo platform, we can load the sub-site and  from there we can launch T-Bioinfo and view areas of analysis. Once this page is loaded, will first use the RNA-seq platform, this starts with choosing  RGenomeGTF to indicate is an uploaded genome with annotation. We will also select FastQ data and Paired Reads with two groups of one each to compare a control against the mutant.
Then we will click start and view the logical graph of the RNA-seq pipeline, once chosen, only those algorithms that are relevant will light up as your are creating your pipeline.

PCR clean to do pre-processing, we can also learn more about pre-processing, and all the buttons will be interactive.
Emer is used for error correction

Tophat for mapping and papers are referenced in this area.
CuffMerge with interactive links so that you can learn more about how the algorithm works.
Bowtie 2 for mapping on the genome
RSEM for mapping statistics and then send the data to the output.
Clicking End saves the Pipeline and then it needs to be named.
And Upload NGS data, then add my svl files that are references to fastq files on the server and then upload the reference genome and the GTF file.

Now this window can be closed and we will click run pipeline.

We are taken to the pipeline details page where we can see the pipeline we just created and the process.
To see what is going on with the pipeline we can refresh or check for the email that will notify you if the pipeline has been finished.

This one is actually running already and will be available in the tutorial section. One can click the tutorials page and find may tutorials,

Additionally the view the Knowledge Center to view the FAQ to get more information on how individual algorithms work along with their citations.
Along with quick run-throughs that can be used for education for the platform.