UTAP: User-friendly Transcriptome Analysis Pipeline

RNA-Seq technology is routinely used to characterize the transcriptome and 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 higher 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 sequences (RNA-Seq and bulk MARS-Seq), and ending with sets of differentially expressed genes. Output files are placed in a structured folder system, and summarization of the results is displayed in a rich and comprehensive report containing dozens of plots, tables and links.


UTAP is licensed under GNU General Public License version 3. License needed for commercial use.


Refael Kohen (until version 1.0.7),

refael.kohen@weizmann.ac.il, refael.kohen@gmail.com

support: utap@weizmann.ac.il

Bioinformatics unit at Life Sciences Core Facilities (LSCF)

Weizmann Institute of Science, Rehovot 76100, Israel.


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