[Genome] BLAT output: how to interpret the numbers when the alignment happened on the negative strand? / Can I specify neg. strand counting in command-line version?

[Rachel Harte]

Anton,

You are correct in saying that the coordinates in the Blat output are
relative to the + strand even if the sequence aligns to the - strand.
Unfortunately, there isn't an option to get output with coordinates
relative to the - strand. You will need to write a script to reformat the
Blat output to give - strand coordinates.

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 Tue, 23 Jan 2007, Anton Kratz wrote:

> Hi,
>
> I have a question regarding BLAT output, how to interpret the numbers when
> the alignment happened on the negative strand.
>
> Let's say I have the genetic sequence on hg17/NCBI35, Chromosome 3, negative
> (!) Strand, starting from 57505108 and going to 57505208 (from 5' to 3'):
> aaaaaccacaagcatgcctatacaccaatagtagacaaacagagagccaaatcatgagtgaactcccatttacaattgctacaaagagaatgaaatacct
>
> When I align this with the online BLAT-Version on
> http://genome.ucsc.edu/cgi-bin/hgBlat against hg17 I expected to get, well,
> something like this as a result:
>
>    ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND
> START    END      SPAN
> ---------------------------------------------------------------------------------------------------
> browser details YourSeq          100     1   100   100 100.0%     3   -
> 57505108  57505208   100
> [...]
>
>
> But actually the first lines of the results page look like this:
>
> BLAT Search Results
>
>    ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND
> START    END      SPAN
> ---------------------------------------------------------------------------------------------------
> browser details YourSeq          100     1   100   100 100.0%     3   -
> 142000533 142000632    100
> [...]
>
> So my first question is: does BLAT display positions in respect to the
> positive strand, even if the alignment was on the negative strand?
>
> If yes: can I somehow make the command-line version of BLAT display the
> positions is the output.psl file in respect to the negative strand?
>
> Best regards,
> Anton
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>