aTAP is a comprehensive bioinformatics web-based platform for analyzing RNA-Seq data. aTAP provides a one-stop service for performing de novo assembly of the RNA-seq data, annotating, and visualizing gene expression from the analysis.
You can follow these steps to start using aTAP to analyze RNA-seq data. For now, aTAP supports only short-read sequencing either single-end or paired-end read.
1. On the landing page, you can click on the "Sign in" button to sign in or request an account for using aTAP. For now, aTAP is freely available for academic users only.
2. If you have already gotten the username and password from the admin, you can log in to the system immediately. On the other hand, if you want to request an account, please select "Click here to register".
3. After you logged in to the system, you can start to create a project, manage a project, and log out. Please select "Create" to start your first project.
4. On this page, you can provide basic information about your project e.g. Genus, Species, Number of conditions, Number of replicates, and the name of experimental conditions.
5. You can select the type of sequencing technology and then upload all files into the system.
6. Then, you can select samples to analyze. If you want to use all samples, just click "select all".
7. Before submitting the job, you can review and adjust the parameters of each bioinformatics workflow. The default values are offered to you. In case of no biological replicate, edgeR is the only option that you can select. On the other hand, DeSeq2 or edgeR are offered, please select on your preference. After finishing this step, please submit the job into the system. It will be automatically queued and processed later.