How to retrieve EST data from UCSC

[diego diaz]

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!

[GenoMax]

What genome build did you have this problem with? Just tried hg19 with chr22 and was able to get BED data back.

Oops. Just saw that your input is in BED format. Let me test that.

[diego diaz]

What genome build did you have this problem with?

I was trying with Mus musculus mm9

[GenoMax]

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.

[Richard Finney]

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 :

http://hgdownload.cse.ucsc.edu//gbdb/genbank/data/processed//genbank.206.0//full

[diego diaz]

Thanks GenoMax and Richard for your help !