Getting a GTF of expressed repeat annotation from Ensembl
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
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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.
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,
dnais unmasked DNA sequence anddna-rmcorresponds to hand masked genomic DNA whereasdan-smis the soft masked DNA sequence. I wish Ensembl Genomic Browser has a clear description of how to get the repeated sequence file.