A fuzzy method for RNA-Seq differential expression analysis in presence of multireads.

ABSTRACT:

Background

When the reads obtained from high-throughput RNA sequencing are mapped against a reference database, a significant proportion of them - known as multireads - can map to more than one reference sequence. These multireads originate from gene duplications, repetitive regions or overlapping genes. Removing the multireads from the mapping results, in RNA-Seq analyses, causes an underestimation of the read counts, while estimating the real read count can lead to false positives during the detection of differentially expressed sequences.

Results

We present an innovative approach to deal with multireads and evaluate differential expression events, entirely based on fuzzy set theory. Since multireads cause uncertainty in the estimation of read counts during gene expression

SUBMITTER: Consiglio A 

PROVIDER: S-EPMC5123383 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature