RepeatMasker for opossum

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yangmu3

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Sep 28, 2022, 12:26:58 PM9/28/22
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Hi,

I'm using the opossum genome version ASM229v1, but on the download page (http://hgdownload.soe.ucsc.edu/downloads.html#opossum) there's only monDom5. 
I would like to run RepeatMasker on ASM229v1. Could you please let me know what were the commands that were used to run the opossum RepeatMasker, and what sequence search engine and repeat database was used for RepeatMasker (also the version of these programs and database)? Thank you very much!


Best regards,
Mu

Hiram Clawson

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Oct 3, 2022, 1:21:25 PM10/3/22
to yangmu3, gen...@soe.ucsc.edu
Good Morning Mu:

Please note, this genome assembly is available in the RefSeq version at:

https://genome.ucsc.edu/h/GCF_000002295.2

With download files available at:

https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/295/GCF_000002295.2/

Specifically the repeat masker output file:


https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/295/GCF_000002295.2/GCF_000002295.2.repeatMasker.out.gz

with version information:

RepeatMasker version development-$Id: RepeatMasker,v 1.332 2017/04/17 19:01:11 rhubley Exp $
Search Engine: Crossmatch [ 1.090518 ]
Master RepeatMasker Database: RepeatMaskerLib.embl - Complete Database: dc20181026-rb20181026

Building species libraries in: Libraries/dc20181026-rb20181026/monodelphis_domestica
- 946 ancestral and ubiquitous sequence(s) for monodelphis domestica
- 124 lineage specific sequence(s) for monodelphis domestica

--Hiram
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