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

ABSTRACT: 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, transcriptome sequencing can be used as a cheaper alternative which already enables to identify SNPs located in transcribed regions. In this paper, we propose a method that identifies, quantifies and annotates SNPs without any reference genome, using RNA-seq data only. Individuals can be pooled prior to sequencing, if not enough material is available from one individual. Using pool

SUBMITTER: Lopez-Maestre H 

PROVIDER: S-EPMC5100560 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature