iCottonQTL – An R/Shiny Web App for Streamlining Cotton Genetic Mapping

Project Information

iCottonQTL, a newly publicly available R/Shiny App, was developed to streamline genetic mapping using community developed SNP arrays to assist in the analysis of multiple populations.  Preprocessing raw [CottonSNPchip] data from biparental populations into a format that is commonly used for linkage mapping, ie with the program JoinMap, for trait association is complicated and error-prone. The iCottonQTL app bundles numerous R functions into a visual interface that simplifies the process for various methods of filtering the raw data and providing multiple forms of output for downstream applications, including the input format for Joinmap.  The app seeks to make biparental analysis more accessible to researchers with less experience with bioinformatic methods.  Additionally, iCottonQTL provides a one click conversion of the data generated from the genotyping arrays to the format for uploading raw data to CottonGen and provides a built-in button for emailing the formatted data directly to CottonGen.  This was designed to provide an easier method for submitting genotyping data from raw chip data to CottonGen to assist with publication requirements.  Submission of this data is extremely useful for future chip development, supporting meta-analysis, and expanding the impact of your published results.


The App can be found herehttps://gbru-ars.shinyapps.io/iCottonQTL/