[Genome] isPcr doesn't find an amplicon?

[Ann Zweig]

Hello Amir,

	When I search for ENSG00000000457 in the Genome Browser, I find two 
transcripts located at: chr1:168,088,839-168,129,717.  Likewise, when I 
look it up on the Ensembl website, they place it at the same location on 
chr1.  Are you working on the latest human assembly: hg18?

	Please give us more details, and we can help clear things up for you.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

We invite you to give us your feedback on the UCSC Genome Browser 
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177




Amir Karger wrote:
> Hi.
> 
> I put the following primer pair into isPcr (command line and web
> version), and got no results. I've confirmed that I can get results with
> other primers, so I know I'm using it correctly.
> 
> ENSG00000000457_E13A_P14        TTCCACCTCCGCGTGC        AGCTTTAGGACCCTC
> 
> isPcr should be finding chr20:59,627,734-59,627,760 on the + strand.
> 
> I've confirmed with the Genome Browser that the forward primer and the
> complement of the reverse primer do appear at those positions on chr20.
> 
> Could you tell me why isPcr isn't finding it? I thought maybe one of the
> primers was a repeat, but at least my command-line version isn't doing
> any masking: I just did isPcr chr20.fa primers.tab primers.fasta.
> 
> Thanks,
> - Amir Karger
> Research Computing
> Life Sciences Division
> Harvard University
> 617-496-0626
> 
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