Getting a GTF of expressed repeat annotation from Ensembl

Question

[akh22]

Hi,

I can generate and download GTF of repeated sequence (mm10) from a USCD table browser by using a RepeatMasker track. Can anybody point me in the right direction to do this with Ensembl browser ? Also, Ensembl has a hand-made, (rather than using RepatMaskter) repeated sequence list ?, and if so how can I download this as well ?

Thanks in advance.

Aki

[GenoMax]

You can take a look at this thread: Repeat masked gtf files from ensembl

AFAI see these files are not available directly from Ensembl.

[akh22]

Thanks. I think I got it. I followed the link you posted and the answer had the clue. It is included in a dan folder in the Fasta DNA dump. According to README, dna is unmasked DNA sequence and dna-rm corresponds to hand masked genomic DNA whereas dan-sm is the soft masked DNA sequence. I wish Ensembl Genomic Browser has a clear description of how to get the repeated sequence file.