[BioC] fixed

Chad Shaw cashaw at bcm.tmc.edu
Wed Aug 6 12:51:56 MEST 2003


Indexing to the ends of genes seems like an error --it makes for 
in the interpretation of CHRLOC.

I went ahead and downloaded UCSC tables and fixed the error in my local 

What I did was: download various UCSC tables, look for - strand genes, 
use the
opposite (largest available) index (start of transcription index) as the 
CHRLOC for the
- strand genes.

Hope this helps.

>>Some biologists I work with are telling me that the
>>-strand CHROMELOCs for mgu74av2 are from the END of the gene,
>>not the begininng.
>I did some study and found that chromosomal location data are indexed from the p 
>to q arm on the +strand but from q to p arm on the -strand, which agrees with 
>what the biologists were telling you. I wrote to a person in UCSC Human Genome 
>project about this but have not get any confirmation back yet. 

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