Repeat masked gtf files from ensembl
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16 months ago

I am looking for a repeat masked version of a reference genome from ensembl. I find information posted here that suggests accessing via ftp. I can't find figure out what subdirectory it might be hiding in. Searching via command-line didn't turn anything up.

I could run repeat-masker myself but as I remember setup is pretty involved (you need to download a repeat library, etc.)

I can post in some ensembl forum if that's more appropriate.

thanks,

ensembl RNA-Seq genome • 960 views
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Repeat masked gtf files from ensembl

Do you actually want a GFF file with regions of the genome that are repeat masked or a repeat masked genome sequence (answer provided by @h.mon below).

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Hi, yes the gff (or gtf) file is what I'm looking for. Something analogous to this file from UCSC.

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Do you mean a GTF or GFF containing the repeats, or just the genes as annotated on repeat-masked sequence?

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Thanks for helping me clarify. I'm looking for a gtf file containing the locations of all masked regions in the ensembl reference genome. It might look like this:

chr1    hg38_rmsk   exon    67108754    67109046    1892.000000 +.  gene_id "L1P5"; transcript_id "L1P5";

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All the gene annotation in Ensembl is done after repeat masking. There are folders of GFF3 and GTF files on the Ensembl FTP site.

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Sorry, it appears to me that these gtf files are for the gene annotation in ensembl rather than an annotation of the masked regions (types of transposable elements, repeats, etc.)

Am I misunderstanding?

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Yes, they are. I was still quite confused by your comment as it said you were after the repeats, but then the line you gave was an exon line, which would suggest you want the genes.

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Ah, I see. think the 'exon' annotation be a confusing shortcut; the actual annotated feature is a LINE-1 element

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16 months ago
h.mon 32k

The easiest way is to go to the organism Ensembl page, e.g. https://www.ensembl.org/Acanthochromis_polyacanthus/Info/Index for the spiny chromis. There, you will find a "Download DNA sequence (FASTA)" link which will take you directly to the ftp folder containing the complete genome, soft-masked genome, and hard-masked genome.