mRNAseq-based Functional and Pathway Analysis in Chicken is Sensitive to the Method Used to Construct the Reference Transcriptome

Abstract Text:

Both genome-based and de novotechniques can be used to build reference transcriptomes from mRNAseq data.  We compared the results of several approaches for building reference transcriptomes on GO and KEGG pathway predictions, starting from raw mRNAseq data.  We discovered that pathway predictions in chicken can vary substantially depending on the reference transcriptome used, and we provide recommendations for which GO database to use as well as techniques for building new reference transcriptomes.

Keywords:

chicken

mRNAseq

gene ontology