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- Title
De novo assembly and analysis of RNA-seq data.
- Authors
Robertson, Gordon; Schein, Jacqueline; Chiu, Readman; Corbett, Richard; Field, Matthew; Jackman, Shaun D.; Mungall, Karen; Sam Lee; Okada, Hisanaga Mark; Qian, Jenny Q.; Griffith, Malachi; Raymond, Anthony; Thiessen, Nina; Cezard, Timothee; Butterfield, Yaron S.; Newsome, Richard; Chan, Simon K.; Rong She; Varhol, Richard; Kamoh, Baljit
- Abstract
We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.
- Subjects
RNA; GENETIC transcription; GENOMICS; GENETIC code; LABORATORY mice
- Publication
Nature Methods, 2010, Vol 7, Issue 11, p909
- ISSN
1548-7091
- Publication type
Article
- DOI
10.1038/nmeth.1517