RepeatMasker data download

Question

[tothepoint]

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.

Answer 1

[Luis Nassar]

Hello,

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 [e-mail]. We do periodically check biostars, in which case, using the UCSC tag is the best way to ensure visibility.