[Genome] EST direction

[Rachel Harte]

Jyoti,

The estOrientInfo table has a field called intronOrientation. If this is 0
and the direction for this EST in the gbCdnaInfo table is 0, then this EST
has unknown direction and will have no arrows when displayed in the EST
track.

You can do this query using the Table Browser. Click on the "Tables" link
on the top blue menu bar and select the genome and assembly of interest.
The EST tracks are in the "mRNA and EST Tracks" group. You can use the
filter button to set up filters on fields of both estOrientInfo table and
the gbCdnaInfo table.

I hope that this helps you. Please let us know if you have further
questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Mon, 22 Jan 2007, Shah, Jyoti K. wrote:

> Hi UCSC team,
> I need your help in interpreting EST data. According to the
> FAQ,direction of arrows indicate the EST direction. However some of the
> ESTs have no arrow indicated on them in the genome browser view (For
> e.g. CV409634). Your previous archives suggest that these ESTs have no
> arrows because they have weaker alignments. I would like to filter out
> such ESTs for my analysis. Where is this information stored?
> Thanks in advance,
> Jyoti
>
>
>
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