Effect of de novo transcriptome assembly on transcript quantification.

ABSTRACT: Correct quantification of transcript expression is essential to understand the functional elements in different physiological conditions. For the organisms without the reference transcriptome, de novo transcriptome assembly must be carried out prior to quantification. However, a large number of erroneous contigs produced by the assemblers might result in unreliable estimation. In this regard, this study investigates how assembly quality affects the performance of quantification based on de novo transcriptome assembly. We examined the over-extended and incomplete contigs, and demonstrated that assembly completeness has a strong impact on the estimation of contig abundance. Then we investigated the behavior of the quantifiers with respect to sequence ambiguity which might be originally prese

SUBMITTER: Hsieh PH 

PROVIDER: S-EPMC6549443 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature