HISAT2 indexes for mm39

HISAT2 indexes for mm39Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019).</p

HISAT2 indexes for chm13v2

HISAT2 indexes for chm13v2 {Kim, 2019}Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37, 907–915 (2019).</p

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 in RepEnTools 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 IGV v2.15 (Integrative Genomics Viewer) {Thorvaldsdottir, 2013}. pHMM – profile Hidden Markov Model.</p

RepEnTools - mm39 RMSK.gtf

mm39 RMSK.gtf for RepEnToolsOnly suitable for mm39Original bed12 file made with repeat masker (www.repeatmasker.org), downloaded from UCSC Table Browser (Karolchik, 2004). Last updated: 2020-07-30The repeat masker (RMSK) annotation file employed in RepEnTools is adjusted to correctly represent the information on the repeat element.</p