Directories:
annotation_data: Contains genomic features (annotation_data/chrom_nums.csvis used to change chrom names).data_from_lit: Holds parental insertion information.relocate_summary_results: RelocaTE2 results for each RIL (files were renamed).scripts: Includes a series of scripts used to transform RelocaTE2 input.
All scripts are ran within the scripts directory
- Reads in all RIL RelocaTE2 results and creates one long table with selected columns.
- Chromosome names are changed, and a
Chr_Startcolumn is created (joining theChrandStartcolumns).- This column contains all possible insertion sites in the sequenced RILs.
- Modifies parental Ping and Pong data.
- Reads in
parental_pings.csvandparental_pongs.csv, subsets columns, and creatsChrom_Startcolumn
- Reads in
- Outputs new file (ex.
parent_ping_loc.tsv), and this will be used when finding Ping locations in RIL populations.
- A goal is to create a summary file that has all possible locations (
Chrom_Start), origin of insertion (de novo or which parent it came from), type of insertion, and a presence/abscence table (1/0 for P/A). - Reads in processed data from scripts above, makes dictionaries (
lines : locations), and compares locations between lines
- No ping locations (from literature) in parental relocate results
- There are 15 ping locations (from literature) in the relocate results
- The origin column has information (A123, EG4, or de novo) depending on if the location is shared with a parental insertion previously called by relocate
- The following command was used to get the origin frequency for the RIL insertions
cut -f 98 | sort | uniq -c
| 8 | A123 |
| 19871 | de novo |
| 2 | EG4 |
| 1 | Origin |