BSA RNA-Seq
Dan Nettleton, Sanzhen Liu, and Patrick S. Schnable
An R script to determine complete linkage
A novel implementation of BSA that uses RNA-Seq data (BSR-Seq) was reported to rapidly and efficiently map genes responsible for mutant phenotypes. BSR-Seq was used to de novo discover single nucleotide polymorphisms (SNPs) and then separately quantify alleles of each SNP in bulked mutant and non-mutant samples. An empirical Bayesian method of analyzing the resulting counting data of alleles was developed to account for biological and technical variation introduced by RNA-Seq. Using this approach it is possible to rapidly and inexpensively map genes responsible for mutant phenotypes to high resolution. The empirical Bayesian approach was implemented using this R script to determine the probability of complete linkage between a genetic marker and the causal gene. The detail of this method was described in the Method section in the paper of Liu et al. 2012.
Download BSR-Seq (2 Kb - 28 SEP 2014)
Citation
Liu S, CT Yeh, HM Tang, DS Nettleton, PS Schnable (2012) Gene mapping via Bulked Segregant RNA-Seq (BSR-Seq).
PLoS ONE, 7(5): e36406.
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Abstract |
Full Text PDF |
Supplemental Materials |
doi:10.1371/journal.pone.0036406
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