Can I use my own GTF file/transcriptome with tappAS?

Users can potentially use any annotation file with tappAS. However, it is required that users functionally annotate the file and re-format it as a tappAS-compatible GFF3. Since this is not a trivial task, we currently provide pre-annotated reference GFF3 files for ENSEMBL and RefSeq for mouse, human and a few other model organisms, but only for some versions of the annotation. We recommend checking the tappAS paper for further information on transcriptome versions and the functional label categories they contain.

What does the term “functional annotation” mean in the…

TappAS s a GFF3-like format for its transcriptome annotation, but it is not exactly the same as just providing a GFF3 file for the transcriptome used for isoform quantification.

When we refer to tappAS annotation file, we are referring to not only traditional transcript annotation, but also to functional annotation. This means that our GFF3 files are formatted to combine both traditional annotation features (transcripts, exons, etc.) and functional labels, including, but not limited to, UTR lengths, CDS positions, predicted PFAM domains, sequence motifs, etc. More details about annotated functional categories and their source databases are available in our tappAS paper. Details about this GFF3-based formatting can be found in the “Projects” section of our website’s Overview page.

Is there any example dataset included in tappAS for…

TappAS includes a Demo dataset that users can load by selecting the option “Demo” upon project creation (see image below). The Installation PDF contains the exact steps to follow to create a Demo project, and this is the dataset that we generally recommend for users to try out the application. It is also the same dataset that is used in our recently published tappAS paper, where users may find more examples of analysis, how to couple them, how to interpret results and the graphics and plots generated by the application.

Where do I find more documentation for tappAS?

TappAS’ website contains an Overview section that describes the necessary inputs to create a project, the application’s computational requirements, the graphical interface, and some of tappAS main features. We are also working on a series of Tutorials demonstrating different aspects of the application and how to run and interpret Functional Iso-Transcriptomics analyses. You can see all currently published tutorials here.

In addition, our team gave a live tutorial on Functional Iso-Transcriptomics (FIT) analysis at ISMB 2020 online conference. If interested in watching the lecture and/or doing the exercises, you can find the part of the tutorial addressing tappAS in this video: The necessary files used during the hands-on, as well as a slides containing all hands-on exercise descriptions, are available here. Note that all files used for this purpose are the same as those provided in the Demo project (see FAQ right below).

Finally, we recommend using the “Help” buttons available in all of tappAS windows and panels. These buttons work as built-in documentation and will provide extra information for whatever it is a user is viewing at the moment: analysis parameters window before running an analysis, a results table, a plot or summary graphics.

How to cite us?

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing

Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Ana Alastrue-Agudo, Pablo Bonilla, Jeremy Newman, Lauren McIntyre, Victoria Moreno-Manzano, Ana Conesa

bioRxiv 690743; doi:

Do you have problems loading our annotations files?

In tappAS 0.99.15, we update some sources and how tappAS works with the annotations files. If you don’t have the lasted version of tappAS your next projects downloading a new annotation will failed. By other hand, your old projects wouldn’t worked with new annotations by the same change.

If you want to update tappAS, you have to delete your old projects and delete your References folder in your tappasWorkspace before run the new version. Then, you can create your old projects again and they will work with the new changes.

Remember that tappAS is still a beta version and changes like this could happen in the future. If you want to update tappAS to version 0.99.15 or lasted and you have a lower version can follow this link.

How to run tappAS with more RAM?

By default tappAS is using 1.7Gb of RAM if your computer has at least 8Gb, but in some cases it isn’t enough to run all analysis. If you have some problems with that you can run tappAS with more RAM if is available.

To do that follow the next steps:

1º Go to tappAS default folder (usually tappas.0.99.xx where xx is your release version)

2º Run the tappas.jar file with the next commant line:

java -XmsAM -XmxBM -jar tappas.jar

Where A and B are the minimum and maximum RAM (in Mb) that you want to give to the app. If you want to give 2Gb as minimun and 6Gb as maximum you need to run:

java -Xms2000M -Xmx6000M -jar tappas.jar

(You need to assign ram in Mb)