Data and code associated with the manuscript "Short tandem repeats delineate gene bodies across eukaryotes" (Reinar et al.)

The "Rev_Pipeline_and_Figures" Jupyter Notebook contains code required to reproduce results and figures in the manuscript including the repetitiveness function run on simulated data to report repetitiveness of A and AT motifs.The repository also includes theTimeTree phylogenetic tree for 891 species (.nwk, "SourceData.Figure1d_2")Relative positions of ULTRA monomer and dimer STRs, and lengths of intergenic sequences (.hdf5, "SourceData.Figure2a_2")Complete repetitiveness analysis with metadata (.tsv, "SourceData.Figure4-5")Transcription factor binding site analyses (.tsv, "SourceData.Figure7e_2")List of housekeeping functions (.txt, "SourceData.Figure7c_2")GO analysis (.tsv, "SourceData.Figure7c_3")The remaining Source Data can be found with the paper.

《Rev_Pipeline_and_Figures》Jupyter Notebook包含复现该论文手稿中所有结果与图表所需的代码，其中包括针对模拟数据运行的重复度分析函数，用于统计A基序与AT基序的重复特性。本数据集仓库还包含以下内容：891个物种的TimeTree系统发育树（文件格式为.nwk，文件标识为"SourceData.Figure1d_2"）；ULTRA单体与二聚体短串联重复序列（Short Tandem Repeat, STR）的相对位置信息及基因间序列长度数据（文件格式为.hdf5，文件标识为"SourceData.Figure2a_2"）；附带元数据的完整重复度分析数据集（文件格式为.tsv，文件标识为"SourceData.Figure4-5"）；转录因子结合位点分析结果（文件格式为.tsv，文件标识为"SourceData.Figure7e_2"）；持家功能清单（文件格式为.txt，文件标识为"SourceData.Figure7c_2"）；基因本体（Gene Ontology, GO）分析结果（文件格式为.tsv，文件标识为"SourceData.Figure7c_3"）。其余源数据可随该论文一并获取。