[Genome] diference between manual and displayed BLAT mapping

[Brooke Rhead]

Hello Ines,

Good question.  We are looking into why these two results are different. 
  However, it may be some time before the person most likely to know the 
answer to this can get to it.  I will let you know what we find out.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


ines mollet wrote:
> Hi,
> the mapping which comes in the tables downloaded from
> UCSC for BF245832 (hg18) has only exons 1 and 2 and
> then a third block which corresponds mostly to exon 17
> with the ag nucleotides of the 3' splice site included
> in the block, which results in a non consensus splice
> site 
> 
> 106	609	4	0	1	8	53	13	89821	+	BF245832	918	1	668	chr11
> 134452384	35117296	35207731	18
> 29,54,14,19,48,104,97,39,30,31,16,23,7,55,20,12,11,5,
> 1,30,84,98,121,196,301,398,437,468,499,515,550,558,613,639,651,663,
> 35117296,35154724,35154779,35154794,35154815,35207249,35207353,35207451,35207491,35207521,35207553,35207570,35207611,35207618,35207674,35207702,35207715,35207726,
> 
> 
> The manual BLAT mapping of this sequence gives
> splicing exons 1,2,16 and 17
> 
> The result of the manual BLAT mapping is better and
> has fewer query inserts - the blocks and positions
> with parenthesis added bellow correspond to the
> mapping of exon 16 which is missing in the mapping
> displayed on the browser
> 
> 635	4	0	1	8	27	14	89795	+	BF245832	918	1	668	chr11
> 134452384	35117296	35207731	20
> 29,54,14,19,48,(12,16),102,97,39,30,31,16,23,7,56,19,12,11,5,
> 1,30,84,98,121,169,182,198,301,398,437,468,499,515,550,558,614,639,651,663,
> 35117296,35154724,35154779,35154794,35154815,(35199827,35199839),35207251,35207353,35207451,35207491,35207521,35207553,35207570,35207611,35207618,35207675,35207702,35207715,35207726,
> 
> 
> Why does this happen? What parameters do you apply in
> a manual BLAT  mapping which make it better than the
> BLAT mappings displayed on the browser?
> 
> 
> Thank you for your attention
> 
> Ines
> 
> 
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