[ensembl-dev] Ensembl REST API | map/:species/:asm_one/:region/:asm_two

[Ramiro Magno]

Hi Devs,

When can I expect an update on this question?

Thank you very much indeed.

Best regards,

Ramiro Magno

On Fri, 13 Sep 2019 at 16:25, Ramiro Magno <ramiro.magno at gmail.com> wrote:

> Hi Devs,
>
> I am trying to understand here the liftover functionality provided by the
> "map/:species/:asm_one/:region/:asm_two" endpoint.
>
> I am getting unexpected results with this endpoint. It could be just
> because of my expectation which is not correct but I'd appreciate some
> clarification.
>
> In attachment you find a csv file with results organised as a table. I've
> asked the api to map some coordinates from GRCh37 to GRCh38. Each column
> ending with "_0" indicates query input data, those columns ending in "_1"
> indicate data I obtained in the json data field named "original", and those
> ending in "_2" indicate data obtained from the json data field named
> "mapped".
>
> In summary:
>
> - Columns "*_0" are my query values, i.e. GRCh37.
> - Columns "*_1" are data from the "original" json object, I expected the
> same values as used in the query, i.e. coordinates in GRCh37 assembly.
> - Columns "*_1" are data from the "mapped" json object, the new
> coordinates as mapped onto the GRCh38 assembly.
>
> I expected coordinates in columns "start_0" and "start_1" to be the same,
> and in columns "end_0" and "end_1" also to be the same. However, this is
> not always the case... It seems that, at times, the values returned in
> "original" and "mapped" have been swapped... I am really confused...
>
> Here's an example:
> https://rest.ensembl.org/map/homo_sapiens/GRCh37/X:10001..60001:1/GRCh38/?coord_system=chromosome;target_coord_system=chromosome
>
> ---
> mappings:
>   -
>     mapped:
>       assembly: GRCh38
>       coord_system: chromosome
>       end: 10001
>       seq_region_name: X
>       start: 10001
>       strand: 1
>     original:
>       assembly: GRCh37
>       coord_system: chromosome
>       end: 60001
>       seq_region_name: X
>       start: 60001
>       strand: 1
>
>
> Many thanks in advance.
>
> All the best, RM
>
>
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