Efficient Approach to Correct Read Alignment for Pseudogene Abundance Estimates.

ABSTRACT: RNA-Sequencing has been the leading technology to quantify expression of thousands of genes simultaneously. The data analysis of an RNA-Seq experiment starts from aligning short reads to the reference genome/transcriptome or reconstructed transcriptome. However, current aligners lack the sensitivity to distinguish reads that come from homologous regions of an genome. One group of these homologies is the paralog pseudogenes. Pseudogenes arise from duplication of a set of protein coding genes, and have been considered as degraded paralogs in the genome due to their lost of functionality. Recent studies have provided evidence to support their novel regulatory roles in biological processes. With the growing interests in quantifying the expression level of pseudogenes at different tissues or ce

SUBMITTER: Ju CJ 

PROVIDER: S-EPMC5514313 | biostudies-literature | 2017 May-Jun

REPOSITORIES: biostudies-literature