Impact of Minimum Motif Length (1 vs. 2) on Homopolymer Detection in Tandem Repeats

This dataset is related to our study on Tandem Repeats. For additional results and detailed information on mouse strains, please refer to https://zenodo.org/records/15313223. The homopolymers_min1_vs_min2.rar archive is primarily intended to compare the effect of setting the minimum motif length to 1 versus 2 on homopolymer detection. The archive contains two subfolders and four files. The colab-repeat-finder subfolder includes the Python files used to run the scripts, with the key script being perfect_repeat_finder.py. The reference subfolder contains the mouse reference genome mm39.fa. Using the example code provided in script_example.txt, two files can be generated: mm39.perfect.repeat.bed and mm39.perfect.repeat.setting1.bed. The file mm39.perfect.repeat.bed corresponds to results obtained with the minimum motif length set to 2, while mm39.perfect.repeat.setting1.bed corresponds to results with the minimum motif length set to 1. The R script compare.R compares homopolymers between these two result files and includes detailed code annotations. The comparison shows that homopolymer detection results are identical whether the minimum motif length is set to 1 or 2.