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Nucleic Acids Res. 2010 Jul;38(12):e131. doi: 10.1093/nar/gkq224. Epub 2010 Apr 14.

Biases in Illumina transcriptome sequencing caused by random hexamer priming.

Author information

1
Division of Biostatistics, School of Public Health, UC Berkeley, 101 Haviland Hall, Berkeley, CA 94720-7358, USA. khansen@stat.berkeley.edu

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.

PMID:
20395217
PMCID:
PMC2896536
DOI:
10.1093/nar/gkq224
[Indexed for MEDLINE]
Free PMC Article

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