UTAP: User-friendly Transcriptome Analysis Pipeline View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran, Dena Leshkowitz

ABSTRACT

BACKGROUND: 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. RESULTS: 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 [Nat Rev Genet 10:57-63, 2009] and bulk MARS-Seq [Science 343:776-779, 2014] 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. CONCLUSION: 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 analyse transcriptome sequence data. More... »

PAGES

154

Journal

TITLE

BMC Bioinformatics

ISSUE

1

VOLUME

20

Author Affiliations

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12859-019-2728-2

DOI

http://dx.doi.org/10.1186/s12859-019-2728-2

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112987476

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30909881


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