UTAP: User-friendly Transcriptome Analysis Pipeline.
BMC Bioinformatics
; 20(1): 154, 2019 Mar 25.
Article
em En
| MEDLINE
| ID: mdl-30909881
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 1057-63, 2009] and bulk MARS-Seq [Science 343776-779, 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.Palavras-chave
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Software
/
Análise de Sequência de RNA
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Perfilação da Expressão Gênica
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Sequenciamento de Nucleotídeos em Larga Escala
Idioma:
En
Ano de publicação:
2019
Tipo de documento:
Article