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.
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.
[ Abstract | Full Text PDF | Supplemental Materials | doi:10.1371/journal.pone.0036406 ]