Dan Nettleton, Sanzhen Liu, and Patrick S. Schnable

This software/script is provided AS IS and without user support

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)


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 ]