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

[Ramiro Magno]

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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