Terrier Experimental Data

This repository contains the data for the application of Terrier to experimental data. See also: https://github.com/rbturnbull/terrier-experimental-dataThere are 8 libraries of transposable elements (TEs) from flatworms. See the following directories:flatworms/Clonorchis_sinensisflatworms/Dicrocoelium_dendriticumflatworms/Fasciola_hepaticaflatworms/Fasciolopsis_buskiflatworms/Schistosoma_haematobiumflatworms/Schistosoma_japonicumflatworms/Schistosoma_mansoniflatworms/Trichobilharzia_regentiSchistosoma mansoni also has a FASTA file with 21 TEs annotated in the NCBI database.There are 51 libraries of TEs from amphibians:amphibians/Allobates_femoralisamphibians/Ambystoma_mexicanumamphibians/Bombina_bombinaamphibians/Bombina_variegataamphibians/Bufo_bufoamphibians/Bufo_gargarizansamphibians/Dendropsophus_ebraccatusamphibians/Discoglossus_pictusamphibians/Eleutherodactylus_coquiamphibians/Engystomops_pustulosusamphibians/Gastrophryne_carolinensisamphibians/Geotrypetes_seraphiniamphibians/Glandirana_rugosaamphibians/Hyalinobatrachium_fleischmanniamphibians/Hyla_sardaamphibians/Hymenochirus_boettgeriamphibians/Leptobrachium_ailaonicumamphibians/Leptobrachium_leishanenseamphibians/Leptodactylus_fallaxamphibians/Limnodynastes_dumeriliiamphibians/Lithobates_catesbeianusamphibians/Lithobates_sylvaticusamphibians/Mantella_aurantiacaamphibians/Microcaecilia_unicoloramphibians/Nanorana_parkeriamphibians/Oophaga_pumilioamphibians/Oophaga_sylvaticaamphibians/Pelobates_cultripesamphibians/Phrynoglossus_myanhesseiamphibians/Phyllomedusa_bahianaamphibians/Pipa_carvalhoiamphibians/Pipa_parvaamphibians/Platyplectrum_ornatumamphibians/Pleurodeles_waltlamphibians/Pseudophryne_corroboreeamphibians/Pyxicephalus_adspersusamphibians/Rana_kukunorisamphibians/Rana_muscosaamphibians/Rana_temporariaamphibians/Ranitomeya_imitatoramphibians/Rhinatrema_bivittatumamphibians/Rhinella_marinaamphibians/Scaphiopus_couchiiamphibians/Scaphiopus_holbrookiiamphibians/Spea_bombifronsamphibians/Spea_hammondiiamphibians/Spea_multiplicataamphibians/Staurois_parvusamphibians/Xenopus_borealisamphibians/Xenopus_laevisamphibians/Xenopus_tropicalisMost amphibian repeat libraries were generated using RepeatModeler version 2.0.4 (excluding the LTR pipeline extensions by Jullien M. Flynn). Ambistoma mexicanum was generated using RepeatModeler version 2.0.5.Each directory contains:a FASTA file with extension .fa with the library of TE sequences.a CSV file with the predictions from Terriera plot comparing the Terrier predictions with the original annotations (XXXXXXX-comparison.png)a plot with the confusion matrix base on the original annotations (XXXXXXX-confusion.png)A summary CSV of the results is found in `summary.csv`.To reproduce the plot in the paper from the summary, run `plot-summary.py`. This script requires the same virtual environment as Terrier.For more instructions, see: https://github.com/rbturnbull/terrier-experimental-dataCreditsTerrier was developed by:Robert TurnbullNeil D. YoungEdoardo TescariLee F. SkerrattTiffany A. KoschIf you use this dataset, cite the Terrier paper. See more information at: https://github.com/rbturnbull/terrier