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You can always download the whole thing and cut out what you want ...
ftp://hgdownload.cse.ucsc.edu/golden...all_est.txt.gz
You may need the gbSeq file, too.
ftp://hgdownload.cse.ucsc.edu/golden...e/gbSeq.txt.gz
This is for mm9.
mm10, hg18, hg19 etc. are available.
The genbank files are here :
Last edited by Richard Finney; 04-29-2015, 02:15 PM.Leave a comment:
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I was able to get sequence (albeit with small number of queries in BED format) with mm9.
Are you using > 1000 regions? That region tool has a limit of 1000. You may need to do multiple queries in that case.Leave a comment:
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I was trying with Mus musculus mm9Originally posted by GenoMax View Post
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How to retrieve EST data from UCSC
Hi all
I have some genomic coordinates, in BED format, that I want to check with ESTs. I tried to download EST data from UCSC, in bed format, but I couldn't. In the table browser, I selected "mRNA and EST" group and "EST" track, then I select BED as input format, but after a while UCSC sends this message: "procedures have exceeded timeout: 1200 seconds, function has ended.". I tried to download the ESTs via ftp too, but only I found them in FASTA format.
Anyone knows how to retrieve EST data from UCSC, in BED format, without using the table browser?
Thanks in advance!
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