On Mon, Nov 25, 2013 at 7:39 AM, Dave Tang <davetingpongtang@gmail.com>wrote:

> On Mon, 25 Nov 2013 19:31:22 +0900, Sean Davis <sdavis2@mail.nih.gov>
> wrote:
>
>  Hi, Dave.
>>
>> There may be multiple issues going on here, so you'll have to do some
>> digging yourself when discrepancies arise like you see here. Working
>> through your first example, keep in mind that neither Ensembl or UCSC are
>> the actual curators of the RefSeq transcripts. NCBI is the source of that
>> annotation. So, if you go to NCBI gene and search for NM_033453 and then
>> play a bit with the Genomic Sequence Viewer, you'll note that the Gene
>> (protein NP_258412.1) is mapped with the coordinates given at UCSC while
>> the mRNA is mapped with the coordinates given by Ensembl. Add to this
>> complication that UCSC does its own mapping of the transcripts (even
>> RefSeq) and you could even have a "unique" set of coordinates given by UCSC
>> (ie., not the same as NCBI or Ensembl).
>>
>
> Hi Sean,
>
> thank you for the prompt reply.
>
> My aim is to have a set of transcript annotations as opposed to gene
> annotations; I don't really mind whether they are RefSeqs or Ensembl
> transcript models. But I keep running into the same problem where the
> coordinates of either Ensembl or RefSeq transcripts are the coordinates of
> the Ensembl gene that encompasses all the transcripts, i.e. the longest
> Ensembl gene. Here's another example:
>
>
> library("biomaRt")
> ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
> #ENST00000398344 is on chr22:24,313,554-24,316,773
> getBM(attributes = c('chromosome_name',
>
>                      'start_position',
>                      'end_position',
>                      'strand'
>                     ),
>                     filters = 'ensembl_transcript_id',
>                     values = 'ENST00000398344',
>                     mart = ensembl)
>   chromosome_name start_position end_position strand
> 1              22       24313554     24322660     -1
>
> #ENST00000430101 is on chr22:24,315,293-24,316,648
> getBM(attributes = c('chromosome_name',
>
>                      'start_position',
>                      'end_position',
>                      'strand'
>                     ),
>                     filters = 'ensembl_transcript_id',
>                     values = 'ENST00000430101',
>                     mart = ensembl)
>   chromosome_name start_position end_position strand
> 1              22       24313554     24322660     -1
>
> Is it possible to obtain genomic coordinates of Ensembl transcript via
> biomaRt?


Hi, Dave.

You'll want to use "transcript_start" and "transcript_end" rather than
"start_position" and "end_position".

Sean

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