A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model.

ABSTRACT: The sequence of the chicken genome, like several other draft genome sequences, is presently not fully covered. Gaps, contigs assigned with low confidence and uncharacterized chromosomes result in gene fragmentation and imprecise gene annotation. Transcript abundance estimation from RNA sequencing (RNA-seq) data relies on read quality, library complexity and expression normalization. In addition, the quality of the genome sequence used to map sequencing reads, and the gene annotation that defines gene features, must also be taken into account. A partially covered genome sequence causes the loss of sequencing reads from the mapping step, while an inaccurate definition of gene features induces imprecise read counts from the assignment step. Both steps can significantly bias interpretation of

SUBMITTER: Orgeur M 

PROVIDER: S-EPMC5827264 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature