Calling Environmentally Induced Mutations in a Highly Inbred Species using RNA-Sequencing Data
- Resource Type
- Authors
- Knight, Montana S.; Doherty, Colleen J.; Nielsen, Dahlia M.
- Source
- Subject
- RNA-Sequencing Data Analysis
Bioinformatic Pipeline
Environmental Mutations
Plants
Inbred Species
SNPs
Variant Calling
- Language
We present a pipeline to identify non-inherited variants from RNA-Sequencing data using software and custom scripts. We focus on the unique precautions to call variants in a highly inbred plant species. This pipeline uses data from highly inbred samples exposed to control and treatment conditions. This pipeline can be applied to investigate how stress conditions can cause mutations to accumulate over time.
This pipeline can be used to identify induced mutations caused by environmental stress conditions. It is particularly useful in studying inbred species. Associated computer code and software commands are available at https://github.com/montana-knight/Calling-Induced-Variants-with-RNA-Seq-Data. This work was supported by a grant from the National Aeronautics and Space Administration (80NSSC19K0146) to Dr. Colleen J. Doherty. This work was also supported in part by NIEHS training grant T32ES007329 (M.K.).