Biases in Illumina transcriptome sequencing caused by random hexamer priming
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Updated: Jun 13, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
Kasper D Hansen1, Steven E Brenner, Sandrine Dudoit
1Division 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.
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