SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.

doi:10.1093/nar/gkw655

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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.

Nucleic acids research - 2 Nov 2016

Lopez-Maestre Hélène, Brinza Lilia, Marchet Camille, Kielbassa Janice, Bastien Sylvère, Boutigny Mathilde, Monnin David, Filali Adil El, Carareto Claudia Marcia, Vieira Cristina, Picard Franck, Kremer Natacha, Vavre Fabrice, Sagot Marie-France, Lacroix Vincent

Abstract excerpt

SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot be applied to non-model species. They are also mostly tailored for whole genome (re-)sequencing experiments, whereas in many cases,...

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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.

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