[BioC] problem with IGH genes in org.Hs.egCHRLOC
francois.pepin at sequentainc.com
Wed Nov 2 04:36:55 CET 2011
On Nov 1, 2011, at 15:08 , Marc Carlson wrote:
> Hi Francois,
> The CHRLOC mappings are based on the data from UCSC, but in order to
> find a match to "28473", the UCSC knownToLocusLink table that we
> download from UCSC every release has to have an entry in it for
> "28473". Unfortunately, it doesn't. In fact, none of the NCBI linked
> UCSC resources seems to have any entries for entrez gene "28473", which
> means that you are probably stuck looking for this value by using
> another resource (one that is not based on UCSC). So I think you really
> do want to try biomart in this particular case.
I hadn't realized UCSC was used for that since the NCBI website also has chromosomal position. I'm not quite sure why UCSC doesn't like these genes. They're not regular genes because they need to be rearranged to make a functional antibodies, but they're otherwise well-known and well-annotated.
BiomaRt works fine in this case.
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