maize_genomic_ecosystem

Scripts used in "The Genomic Ecosystem of Transposable Elements in Maize," Stitzer et al., 2021

Interactive distributions of raw data of each TE family at https://mcstitzer.shinyapps.io/maize_te_families/

GenomeInfo.R is sourced by R scripts in each directory, provides consistent name variables, and contains the full paths to genome fastas and TE annotations (most of the time - some paths are hard coded in the following directories)

• age_model/ predicts age using a random forest model
• base_composition/ finds methylatable sequence in TE and flanking regions
• diversity/ finds number of segregating sites within each TE copy, and flanking sequence
• figures/ has code for generating manuscript figures
• genes/ finds closest genes, and their expression across developmental atlases
• methylation/ finds DNA and histone methylation of TEs and flanking regions
• mnase/ finds overlap of TEs and flank to MNase hypersensitive regions
• recombination/ identifies the recombinational environment the TE is found in
• subgenomes/ assigns each TE to a subgenome
• te_age/ determines the age of each TE copy
• te_characteristics/ identifies features specific to the TE copy encoded within the gff, like TE length
• te_expression/ calculates the per-copy TE expression level across developmental atlases
• te_genes/ identifies TE genes within each TE model