Data/hora: 09/06/2024 08:28:16

Provedor de dados: | 74
País: | Brazil
Título: | The combined analysis as the best strategy for Dual RNA-Seq mapping
Autores: | Espindula,Eliandro; Sperb,Edilena Reis; Bach,Evelise; Passaglia,Luciane Maria Pereira.
Data: | 2019-01-01
Ano: | 2019
Palavras-chave: | Dual RNA-Seq; Sequential analysis; Combined analysis; Mapping strategies.
Resumo: | Abstract In Dual RNA-Seq experiments the simultaneous extraction of RNA and analysis of gene expression data from both interacting organisms could be a challenge. One alternative is separating the reads during in silico data analysis. There are two main mapping methods used: sequential and combined. Here we present a combined approach in which the libraries were aligned to a concatenated genome to sort the reads before mapping them to the respective annotated genomes. A comparison of this method with the sequential analysis was performed. Two RNA-Seq libraries available in public databases consisting of a eukaryotic (Zea mays) and a prokaryotic (Herbaspirillum seropediceae) organisms were mixed to simulate a Dual RNA-Seq experiment. Libraries from real Dual RNA-Seq experiments were also used. The sequential analysis consistently attributed more reads to the first reference genome used in the analysis (due to cross-mapping) than the combined approach. More importantly, the combined analysis resulted in lower numbers of cross-mapped reads. Our results highlight the necessity of combining the reference genomes to sort reads previously to the counting step to avoid losing information in Dual RNA-Seq experiments. Since most studies first map the RNA-Seq libraries to the eukaryotic genome, much prokaryotic information has probably been lost.
Tipo: | Info:eu-repo/semantics/article
Idioma: | Inglês
Identificador: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000500803
Editor: | Sociedade Brasileira de Genética
Relação: | 10.1590/1678-4685-gmb-2019-0215
Formato: | text/html
Fonte: | Genetics and Molecular Biology  v.42 n.4 2019
Fonte: | info:eu-repo/semantics/openAccess