ArticleBiology open2018
A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model.
Article in Biology open, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Assessing evolutionary and developmental transcriptome dynamics in homologous cell types.Developmental dynamics : an official publication of the American Association of Anatomists · 2022Article
- The Diverse Major Histocompatibility Complex Haplotypes of a Common Commercial Chicken Line and Their Effect on Marek's Disease Virus Pathogenesis and Tumorigenesis.Frontiers in immunology · 2022Article
- Revisiting avian 'missing' genes from de novo assembled transcripts.BMC genomics · 2019Article
- Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.GigaScience · 2018Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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 RNA-seq data. Here, we describe a dual transcript-discovery approach combining a genome-guided gene prediction and a
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