[HTML][HTML] UTAP: user-friendly transcriptome analysis pipeline
BMC bioinformatics, 2019•Springer
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 …
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 …
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.
Springer