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, researchers at the Weizmann Institute of Science developed an intuitive and scalable transcriptome pipeline that executes the full process, starting from cDNA sequences derived by RNA-Seq and bulk MARS-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.

This 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 analyse transcriptome sequence data.


Flow of analysis step performed by the UTAP pipeline. Note that steps that take place only in the MARS-Seq pipeline are shown within broken-line rectangles

Availability – Information about where to download the UTAP Docker application can be found at https://utap.readthedocs.io

Kohen R, Barlev J, Hornung G, Stelzer G, Feldmesser E, Kogan K, Safran M, Leshkowitz D. (2019) UTAP: User-friendly Transcriptome Analysis Pipeline. BMC Bioinformatics 20(1):154. [article]

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