Effect of method of deduplication on estimation of differential gene expression using RNA-seq.

ABSTRACT:

Background

RNA-seq is a useful tool for analysis of gene expression. However, its robustness is greatly affected by a number of artifacts. One of them is the presence of duplicated reads.

Results

To infer the influence of different methods of removal of duplicated reads on estimation of gene expression in cancer genomics, we analyzed paired samples of hepatocellular carcinoma (HCC) and non-tumor liver tissue. Four protocols of data analysis were applied to each sample: processing without deduplication, deduplication using a method implemented in SAMtools, and deduplication based on one or two molecular indices (MI). We also analyzed the influence of sequencing layout (single read or paired end) and read length. We found that deduplication without MI greatly affects estimated

SUBMITTER: Klepikova AV 

PROVIDER: S-EPMC5357343 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature