Re: [GUSDEV] LoadBLATAlignment and gaptables

[Y. T. G. <yon...@pc...>]

Hi Sucheta:
What version of the plugin are you using? The latest version (1.35) has 
gapTableSpace as a command line option, and it is optional.

When we load BLAT alignments of cDNAs, we may take into consideration 
alignments that span or fall on the edge of a gap in the genomic sequence. 
We usually import the per chromosome gap tables from GoldenPath into a 
temporary table space. The temp table space (e.g. ygan is my personal 
schema) needs to be separate from GUS schemas as DDL operations to them 
are restricted and the number and names of gap tables change from version 
to version. The gap information is only used to classify alignments into 
one of 4 categories: very good alignments, very good but contain/close to 
genomic gaps, good, and others.

That said, you may not care about gaps at all or can safely ignore 
the impact of gaps in your case. As of a version later than the one you 
have, you do not have to worry about gap tables any more - just do not 
set the gapTableSpace option in the command line.

-Thomas

On Fri, 29 Apr 2005, Sucheta Tripathy wrote:

> Dear group,
>
> I am trying to use the plugin LoadBLATAlignment, but can't figure out where 
> to define my gaptable(as I see in line 452
>
> 452     my $gapTable = 'ygan.' . $ext_genome_ver . '_' . $target_id . '_gap'
>    ;)
>
> If I have to define a table for gap regions, can anyone please suggest what 
> are the fields.
>
> Do I need to pre-load some data into them?
>
> Many thanks
>
> Sucheta
>
>
>
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