RNaseIII and T4 polynucleotide Kinase sequence biases and solutions during RNA-seq library construction.

ABSTRACT:

Background

RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement. However, the RNA-seq sequence data can be biased during library constructions resulting in incorrect data for SNP, splice junction, and gene expression studies. Here, we developed new library preparation methods to limit such biases.

Results

A whole transcriptome library prepared for the SOLiD system displayed numerous read duplications (pile-ups) and gaps in known exons. The pile-ups and gaps of the whole transcriptome library caused a loss of SNP and splice junction information and reduced the quality of gene expression results. Further, we found clear seq

SUBMITTER: Lee C 

PROVIDER: S-EPMC3710281 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature