GTF files for annotating transposable elements in Capra hircus (goat) genome

Transposable elements (TEs, also called transposons) are mobile genetic elements consist of repetitive sequences, accounting for about half of a mammal genome. TEs are somewhat overlooked in typical genomic and transcriptomic analyses due to its repetitive nature, rendering complexities and uncertainty in attributing ambiguously aligned short reads to the exact elements. In less studied species like Capra hircus (goat), the genomic features of TEs are not well annotated. To benefit TEs research in Capra hircus, we generated detailed annotation files for goat TEs at both subfamily and location levels. The Ensembl curated Capra hircus genome assembly ARS1 (GCA_001704415.1, accessed at https://ftp.ensembl.org/pub/release-112/fasta/capra_hircus/dna/Capra_hircus.ARS1.dna.toplevel.fa.gz,) was used for genome mapping and annotation. The TEs of the Capra hircus genome were annotated using the RepeatMasker (version 4.1.6) software, with default mode run using rmblastn (version 2.14.0+) and FamDB (RBRM 3.8). The RepeatMasker annotation tables were parsed to filter out repeats like rRNA, scRNA, snRNA, srpRNA, and tRNA. The makeTEgtf.pl script (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/makeTEgtf.pl.gz) was used to reformat RepeatMasker table into GTF file for further use. Detailed codes for making and using these files were attached in the Code_for_goat_TE.txt file.