This codebook.txt file was generated on by ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Setaria viridis ME034V TE annotation table 2. Author Information Principal Investigator Contact Information Name: Andrew Read Institution: Univeristy of Minnesota Email: read0094@umn.edu ORCID: 0000-0003-1789-6571 Associate or Co-investigator Contact Information Name: Liang Zhikai Institution: University of Minnesota Email: liang795@umn.edu ORCID: 3. Date of data collection 20201220 4. Geographic location of data collection (where was data collected?): 5. Information about funding sources that supported the collection of the data: -------------------------- SHARING/ACCESS INFORMATION -------------------------- Recommended citation for the data: Read, Andrew; Liang, Zhikai. (2021). Setaria viridis ME034V TE annotation table. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/32ca-4m22. 1. Licenses/restrictions placed on the data: CC BY-NC-ND 3.0 US 2. Links to publications that cite or use the data: https://doi.org/10.11.101/2022.01.05.474142 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? no If yes, list source(s): --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Svm_STRUCT_TE_MINIMAL.bed Short description: bed format file of structurally annotated transposable elements in the Setaria viridis ME034V genome. centromeric, telomeric, and simple repeats were stripped from the raw EDTA output to generate this MINIMAL file B. Filename: Svm_HomologyTE_MINIMAL.bed Short description: bed format file of homology annotated transposable elements in the Setaria viridis ME034V genome centromeric, telomeric, and simple repeats were stripped from the raw EDTA output to generate this MINIMAL file C. Filename: Readme Short description: Description of data 2. Relationship between files: 3. Additional related data collected that was not included in the current data package: 4. Are there multiple versions of the dataset? no If yes, list versions: Name of file that was updated: i. Why was the file updated? ii. When was the file updated? Name of file that was updated: i. Why was the file updated? ii. When was the file updated? -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: https://doi.org/10.1186/s13059-019-1905-y The EDTA TE annotation pipeline was used for homology and structural annotation 2. Methods for processing the data: 3. Instrument- or software-specific information needed to interpret the data: 4. Standards and calibration information, if appropriate: 5. Environmental/experimental conditions: 6. Describe any quality-assurance procedures performed on the data: 7. People involved with sample collection, processing, analysis and/or submission: ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Svm_STRUCT_TE_MINIMAL.bed ----------------------------------------- 1. Number of variables: 2. Number of cases/rows: 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: Description: Value labels if appropriate ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Svm_HomologyTE_MINIMAL.bed ----------------------------------------- 1. Number of variables: 2. Number of cases/rows: 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List A. Name: Description: Value labels if appropriate