[Genome] question on downloading est/genomic alignments info

[Brooke Rhead]

Hello Qu,

To get to the table corresponding to the track "Human ESTs" in the 
Genome Browser, make the following selections in the Table Browser:

(assuming you are using the latest human assembly)

clade: vertebrate
genome: human
assembly: Mar. 2006
group: mRNA and EST tracks
track: Human ESTs
table: est

Note that this is a very large table.  If you plan to download all of 
it, I recommend using the "gzip compressed" option for your output.  
Alternatively, the table is split into chromosomes on our downloads 
page, here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/
the files are named chr1_est.txt.gz, chr2_est.txt.gz, etc.

It is possible for an EST to map to more than one location.  From the 
details page for the track:

"When a single EST aligned in multiple places, the alignment having the 
highest base identity was identified. Only alignments having a base 
identity level within 0.5% of the best and at least 96% base identity 
with the genomic sequence were kept."

You can get to the details page by clicking on the blue track name link 
on the main Genome Browser display page.

I hope this information is helpful.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Qu Zhang wrote:
> Hi there,
>
> I am trying to download the EST/genomic alignment information for all
> human-EST, but I can't find the right option in Table browser. Could you
> tell me what I can do to get that information? Another question is that is
> it possible that an EST is mapped to more than one location in the genome?
> Many thanks for your help!
>
> Best,
> Qu
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