Biases in Illumina transcriptome sequencing caused by random hexamer priming

Kasper D. Hansen, Steven E. Brenner, Sandrine Dudoit

Research output: Contribution to journalArticlepeer-review

Abstract

Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias is independent of organism and laboratory and impacts the uniformity of the reads along the transcriptome. We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias.

Original languageEnglish (US)
Article numbergkq224
Pages (from-to)e131
JournalNucleic acids research
Volume38
Issue number12
DOIs
StatePublished - Apr 14 2010
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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