Regarding the use of Ensembl REST API for converting coordinates between assemblies

Question

[fmerkal]

Hello everyone,

I am broadly interested in looking at the properties of specific sequences from the pig genome, from Ensembl. I aligned my short reads (obtained from a RNA-seq experiment) to an old version of this genome (Sscrofa10.2, new version is Sscrofa11.1). After getting my BAM files, from the alignment, I proceeded to conduct my analysis and obtain a list containing my genomic coordinates of interest.

I used the coordinates from this list as the input for the sequence/region/:species/:region feature of Ensembl REST API to get the sequences. However, this is where I noticed that the genome that was being used for obtaining the genomic sequences associated with my coordinates was Sscrofa11.1. Having realized this I decided to convert my Sscrofa10.2 genomic coordinates to Sscrofa11.1 coordinates using map/:species/:asm_one/:region/:asm_two with curl. Here is an example for one case:

curl 'http://rest.ensembl.org/map/sus_scrofa/Sscrofa10.2/7:129864618..129864690:-1/chromosome:Sscrofa11.1?' -H 'Content-type:application/json'

It seems that I am unable to convert the genomic coordinates between these two assemblies and I get the following error message:

{"error":"Unknown coordinate system:name='chromosome' version='Sscrofa10.2'"}

I have tried different iterations of the curl input line but still nothing. I am wondering if map/:species/:asm_one/:region/:asm_two can only be used with assemblies from a subset of species and that pig is just not one of them. If anyone has any input on this issue or can maybe tell me if I am doing something wrong, I would greatly appreciate it.

Cheers, Fjodor

Answer 1

[Ben_Ensembl]

Hi Fjodor,

You are using the mapping endpoint correctly, but this endpoint only works for a subset of species (human, mouse, zebrafish, rat, dog, C. elegans, S. cerevisiae plus other non-vertebrate species). Unfortunately, pig is not one of the species supported by the assembly convertor endpoint.

However, we do have archives of the REST API from Ensembl 87 onwards e.g e87.rest.ensembl.org. Ensembl 87 contained the Sscrofa10.2 assembly and annotation, so you do not necessarily need to convert to the latest assembly.

Best wishes

Ben Ensembl Helpdesk