Protocols

Genome-wide enrichment of endogenous DNA from non-invasive samples from Snyder-Mackler et al

     Protocol for RNA bait generation

     Protocol for hybridization and library prep

Software and tools

Mixed model Association for Count data via Augmentation from Lea, Tung, and Zhou

     MACAU (binomial mixed model with kinship/population structure controls, for bisulfite sequencing studies) is maintained by our collaborator Xiang Zhou (University of Michigan Biostatistics). You can download the software and user manual here.

WHODAD from Snyder-Mackler et al.

     WHODAD (software for paternity assessment and pedigree ascertainment from low coverage resequencing data) is maintained by our collaborator Xiang Zhou (University of Michigan Biostatistics). You can download the software and user manual here.

Bisulfite sequencing simulator/power analysis (R Shiny app from Lea et al, forthcoming)

     This R Shiny app interactively simulates bisulfite sequencing read counts and performs power analysis using a variety of common modeling approaches for DNA methylation analysis. You can download the app, example input files, and instructions here, or the instructions/readme file on its own here.

     If you use this app in published work, please cite: Lea, A.J., Vilgalys, T.P., Durst, P.A.P., and Tung, J. Maximizing ecological and evolutionary insight from bisulfite sequencing data sets. bioRxiv: dx.doi.org/10.1101/091488

Genome-wide quantification of the effects of DNA methylation on gene regulation (mSTARR-seq) from Lea et al.

     Complete protocol

     

     *The mSTARR-seq CpG-free plasmid, pmSTARRseq is also freely available in the Addgene repository. Get your aliquot here!

Tung lab reduced representation bisulfite sequencing (RRBS) protocol