[Genome] BLAT output format

[Rachel Harte]

Hello Morgane,

There is a reason for this - the PSL format uses 0-based starts so base
positions 1 is represented as 0. See:
http://genome.ucsc.edu/FAQ/FAQtracks#tracks1

The reason for this is it makes it easier to calculate the size of a
region by just subtracting the start from the end without having to add 1.

Please let us know if you have further questions.

Rachel


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


On Thu, 15 Mar 2007, Morgane THOMAS-CHOLLIER wrote:

> Hello,
>
> I'm writing concerning the BLAT ouput formats. I have noticed that the
> chromosomal positions displayed in the psl format have an additional
> nucleotide, compared to the hyperlink format.
>
> For instance, when querying BLAT with this mouse sequence,
>
> tgctgaggaagcctacaccagaacttgcaagtggcttgcaTGATGGATGGGctggtggatagatggatggatgggcttggagacagatgga
>
> I obtain with hyperlink:
>
>           91     1    91    91 100.0%     4   -  140565363 140565453     91
>
>
> But I obtain with psl:
>
> 	91	0	91	chr4		140565362	140565453
>
>
> The start positions are not the same, and the psl format have an
> additional nucleotide.
>
> Is there a specific reason for this difference ?
>
> Thank you in advance for your answer,
>
> Best regards,
>
> Morgane Thomas-Chollier.
>
> --
> **********************************************************
> Morgane THOMAS-CHOLLIER, PHD Student (mthomasc at vub.ac.be)
>
> Vrije Universiteit Brussels (VUB)
> Laboratory of Cell Genetics
> Pleinlaan 2
> 1050 Brussels
> Belgium
>
>
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