UTAP: User-friendly Transcriptome Analysis Pipeline

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...

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Published in:BMC bioinformatics Vol. 20; no. 1; pp. 154 - 7
Main Authors: Kohen, Refael, Barlev, Jonathan, Hornung, Gil, Stelzer, Gil, Feldmesser, Ester, Kogan, Kiril, Safran, Marilyn, Leshkowitz, Dena
Format: Journal Article
Language:English
Published: London BioMed Central 25.03.2019
Springer Nature B.V
BMC
Subjects:
Algorithms
Bioinformatics
Bioinformatics workflow
Biomedical and Life Sciences
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Data analysis
Data processing
Differentially expressed genes
Gene expression
Gene Expression Profiling - methods
Gene sequencing
Genetic engineering
Genomes
Genomics
Genotypes
High-Throughput Nucleotide Sequencing - methods
Life Sciences
Microarrays
NGS
Packaging
Ribonucleic acid
RNA
RNA-Seq
Sequence analysis pipeline
Sequence Analysis, RNA - methods
Software
Transcriptome
Transcriptome analysis
User interface
Differentially expressed genes
RNA-Seq
Transcriptome
Bioinformatics workflow
Normalization
NGS
Sequence analysis pipeline
Genome mapping
Bulk MARS-Seq
UMI (unique molecular identifier)
Gene expression profile
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary: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 T ranscriptome A nalysis P ipeline (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.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-019-2728-2