| Registro completo |
| Provedor de dados: |
Genet. Mol. Biol.
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| País: |
Brazil
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| Título: |
The combined analysis as the best strategy for Dual RNA-Seq mapping
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| Autores: |
Espindula,Eliandro
Sperb,Edilena Reis
Bach,Evelise
Passaglia,Luciane Maria Pereira
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| Data: |
2019-01-01
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| Ano: |
2019
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| Palavras-chave: |
Dual RNA-Seq
Sequential analysis
Combined analysis
Mapping strategies
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| 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.
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| Tipo: |
Info:eu-repo/semantics/article
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| Idioma: |
Inglês
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| Identificador: |
http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000500803
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| Editor: |
Sociedade Brasileira de Genética
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| Relação: |
10.1590/1678-4685-gmb-2019-0215
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| Formato: |
text/html
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| Fonte: |
Genetics and Molecular Biology v.42 n.4 2019
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| Direitos: |
info:eu-repo/semantics/openAccess
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