[Genome] Content filtered message notification

[Ann Zweig]

Hello Enrique,

	You are correct.  All start coordinates in our database are 0-based, not 
1-based. See the explanation in our FAQs: 
http://genome.ucsc.edu/FAQ/FAQtracks#tracks1

	Please let us know if you have more questions about the browser or the 
underlying data.


Regards,

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




> Subject:
> alignment: refGene table
> From:
> "Muro, Enrique" <emuro at ohri.ca>
> Date:
> Wed, 13 Dec 2006 14:54:56 -0500
> To:
> <genome at soe.ucsc.edu>
> 
> 
> Hi, I found this,
> 
> in the table refGene.txt (hg18) I have the next line for NM_000302
> 
> 84      NM_000302       chr1    +       11917332        11958180        
> 11917423
>         11957452        19      
> 11917332,11930619,11932416,11933000,11935266,119
> 37473,11939560,11940485,11941159,11943289,11946175,11946818,11947287,11948123,11
> 948894,11949630,11953313,11955515,11957296,     
> 11917499,11930711,11932550,11933
> 164,11935379,11937537,11939658,11940587,11941291,11943411,11946280,11946944,1194
> 7429,11948237,11948960,11949735,11953460,11955641,11958180,     0       
> PLOD1
> cmpl    cmpl    0,1,0,2,1,0,1,0,0,0,2,2,2,0,0,0,0,0,0,
> 
> 
> 
> if I blat the sequence 
> (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=32307143#sequence_32307143 
> <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=32307143#sequence_32307143>)
> I will obtain the next alignment:
> browser details YourSeq         2986     1  3004  3004 100.0%     1   
> +   11917333  11958181  40849
> 
> instead of chr1    +       11917332        11958180 (the one in the 
> refGene.txt table)
> 
> 
> I have not checked it with more refseqs entries but It seems to me that 
> the table is not
> providing the genome coordinates [1, n] but the location in an array [0, 
> n-1]
> 
> thanks,
> Enrique Muro
> 
> 
> 
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