Getting a GTF of expressed repeat annotation from Ensembl

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4.7 years ago

akh22 ▴ 120

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

RNA-Seq sequence • 2.0k views

ADD COMMENT • link 4.7 years ago by akh22 ▴ 120

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

AFAI see these files are not available directly from Ensembl.

ADD REPLY • link 4.7 years ago by GenoMax 148k

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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.

ADD REPLY • link 4.7 years ago by akh22 ▴ 120

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