| Autor: |
Venkat Sundar Gadepalli, Hatice Gulcin Ozer, Ayse Selen Yilmaz, Maciej Pietrzak, Amy Webb |
| Jazyk: |
angličtina |
| Rok vydání: |
2019 |
| Předmět: |
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| Zdroj: |
BMC Bioinformatics, Vol 20, Iss S24, Pp 1-7 (2019) |
| Druh dokumentu: |
article |
| ISSN: |
1471-2105 |
| DOI: |
10.1186/s12859-019-3251-1 |
| Popis: |
Abstract Background RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high performance computing environment. Results Developed as a tool by the Bioinformatics Shared Resource Group (BISR) at the Ohio State University, we have applied the pipeline to a few publicly available RNAseq datasets downloaded from GEO in order to demonstrate the feasibility of this workflow. Source code is available here: workflow: https://code.bmi.osumc.edu/gadepalli.3/BISR-RNAseq-ICIBM2019 and shiny: https://code.bmi.osumc.edu/gadepalli.3/BISR_RNASeq_ICIBM19. Example dataset is demonstrated here: https://dataportal.bmi.osumc.edu/RNA_Seq/. Conclusion The workflow allows for the analysis (alignment, QC, gene-wise counts generation) of raw RNAseq data and seamless integration of quality analysis and differential expression results into a configurable R shiny web application. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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