UTAP: User-friendly Transcriptome Analysis Pipeline

RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such as Illumina Next-Seq have yielded easy-to-operate machines, with high throughput, at a lower price per base. However, processing this data requires bioinformatics expertise to tailor and execute specific solutions for each type of library preparation.

In order to enable fast and user-friendly data analysis, we developed an intuitive and scalable transcriptome pipeline that executes the full process; starting from cDNA sequences derived by RNA-Seq (supporting various protocols including TruSeq, bulk MARS-Seq and SCRB-Seq) and ending with sets of differentially expressed genes. Output files are placed in structured folders, and results summaries are provided in rich and comprehensive reports, containing dozens of plots, tables and links. In addition, the pipeline supports analysis of Ribo-Seq, ChIP-Seq and ATAC-Seq. UTAP installation is a single singularity image which contains miniconda environment with all software and applications required for running the pipelines and the ability to leverage from cluster resources.

Our User-friendly Transcriptome Analysis Pipeline (UTAP) is an open source, web-based intuitive platform available to the biomedical research community, enabling researchers to efficiently and accurately analyses transcriptome sequence data.