Dear friends, I was downloading repeatmasker data from UCSC. If anyone know about the availability of Capra hircus (goat) repeatmasker data do share the information. I am trying running RepeatMasker on goat in server but it is taking much time.
We have built assembly hubs for many assemblies (including goat), these include RM tracks: https://genome.ucsc.edu/h/GCF_001704415.1
That download data can be found in the following directory: https://hgdownload.soe.ucsc.edu/hubs/GCF/001/704/415/GCF_001704415.1/bbi/
There you will see a few different repeat masker files which correspond to the different repeat element tracks:
GCF_001704415.1_ARS1.rmsk.DNA.bb 26-Jan-2020 21:47 18M GCF_001704415.1_ARS1.rmsk.LINE.bb 26-Jan-2020 21:47 72M GCF_001704415.1_ARS1.rmsk.LTR.bb 26-Jan-2020 21:47 25M GCF_001704415.1_ARS1.rmsk.Low_complexity.bb 26-Jan-2020 21:48 4.2M GCF_001704415.1_ARS1.rmsk.Other.bb 26-Jan-2020 21:48 528K GCF_001704415.1_ARS1.rmsk.RNA.bb 26-Jan-2020 21:48 718K GCF_001704415.1_ARS1.rmsk.SINE.bb 26-Jan-2020 21:47 86M GCF_001704415.1_ARS1.rmsk.Satellite.bb 26-Jan-2020 21:48 8.9M GCF_001704415.1_ARS1.rmsk.Simple.bb 26-Jan-2020 21:48 20M
Keep in mind these are bigBed files, if you are unfamiliar with that format you can find more information here: http://hgdownload.soe.ucsc.edu/downloads.html#gbdb
If you have any further questions, you can email us at email@example.com. We do periodically check biostars, in which case, using the UCSC tag is the best way to ensure visibility.