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Nat Methods. 2013 Jan;10(1):71-3. doi: 10.1038/nmeth.2251. Epub 2012 Nov 18.

Streaming fragment assignment for real-time analysis of sequencing experiments.

Author information

1
Department of Computer Science, University of California, Berkeley, Berkeley, California, USA.

Abstract

We present eXpress, a software package for efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. We demonstrate its use on RNA-seq data and show that eXpress achieves greater efficiency than other quantification methods.

PMID:
23160280
PMCID:
PMC3880119
DOI:
10.1038/nmeth.2251
[Indexed for MEDLINE]
Free PMC Article

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