title: Biases in Illumina transcriptome sequencing caused by random hexamer priming.
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.
authors.affiliation: Division of Biostatistics, School of Public Health, UC Berkeley, 101 Haviland Hall, Berkeley, CA 94720-7358, USA. khansen@stat.berkeley.edu
authors.forename: Kasper D
authors.initials: KD
authors.lastname: Hansen
authors.forename: Steven E
authors.initials: SE
authors.lastname: Brenner
authors.forename: Sandrine
authors.initials: S
authors.lastname: Dudoit
mesh_terms: D017931:DNA Primers; D020869:Gene Expression Profiling; D009711:Nucleotides / Q000032:analysis; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D009711:Nucleotides
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