Hello,
I used the UCSC table browser to extract a BED file with exon coordinates
for a list of genes.
When I tried working with the file, I realized that there was an error in
the coordinates.
Lines x to y refer to gene NM_001848 (COL6A2).
While the RefSeq gene name is correct in the file (NM_001848_exon_#), the
coordinates that are associated with that gene map to NM_206962.1, an
adjacent gene (PRMT2) on chromosome 21.
I further went on to notice that the file contained aditional COL6A2
transcripts which coordinates mapped outside chromosome 21, therefore I was
constantly getting an error message when trying to use this file.
When I made a query for the COL6A2 coordinates with the one isolated gene
identifier, the BED file output was correct. I.e., I do not understand why
the original output did not work correctly.
Thank-you,
Chris Dias
UBC
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