Re: [GUSDEV] LoadBLATAlignment and gaptables

[Sucheta T. <su...@vb...>]

Hi Thomas,

Thanks for the reply. I am using the older version of the plugin, I will
update it..

In fact, now I forced the alignments to be loaded even without the
gaptables, by assigning some return values in BLAT::Alignment file. I
guess it is not the right way to do.

Another question I have is, with the new plugin, is there a possibility
that some of the alignments will be thrown out, if it does not belong to
these 4 categories? In this particular instance I found atleast some of
the alignments are thrown out, and also if the alignments that are not
loaded, are they stored in some file for look up later.

Many thanks

Sucheta
> 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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>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606