RepEnTools - Cleaned RMSK.gtf for analysis

Cleaned RMSK.gtf for RepEnToolsOnly suitable for chm13v2Original bed12 file from {Hoyt, 2022}, made with repeat masker {www.repeatmasker.org}, downloaded from UCSC Table Browser {Karolchik, 2004}. Version: hub_3671779The repeat masker (RMSK) annotation file employed<b> </b>in <i>RepEnTools</i> is adjusted to correctly represent the annotated repeat element boundaries (e.g. red element). The UCSC Table Browser allows retrieval of the RMSK files generated specifically for chm13v2 {Hoyt, 2022; Karolchik, 2004 10.1093/nar/gkh103}. While the BigBed file displays the elements with correct annotations, visualising the unpacked version (bed12) reveals both the pHMM model used by RMSK (thin) and the actual annotated segment (thick). Notably, the UCSC gtf output reflects only the pHMM model, not the true repeat element (vertical red dashed line). To adjust the annotation file, we extracted the exons as gtf, sorted and merged overlapping annotations of identical name twice (in-house script), and performed table operations. Browser views generated using <i>IGV v2.15 </i>(<i>Integrative Genomics Viewer</i>) {Thorvaldsdottir, 2013}. pHMM – profile Hidden Markov Model.