Seeking Tool to Convert Chromosome Coordinates to cDNA Coordinates for Arabidopsis

Question

[remagen]

Hello everyone,

I am currently working on a project involving Arabidopsis thaliana and need assistance with converting chromosome coordinates to cDNA coordinates. I have the following data:

chr    strand    pos
chr4   +         13027892
chr4   -         13487630

I haven't been able to find suitable tools or resources to perform this conversion. If you have any suggestions or guidance on this topic, I would be grateful for your input.

Thank you in advance for your help!

[Pierre Lindenbaum]

Mapping between genomic coordinates to transcriptomic coordinates

[b.contreras.moreira]

Not direct, but you could use https://rest.ensembl.org if your genome assembly is GCA_000001735.1. Using your example data you can build the following URL to find out which transcripts overlap with some genomic coordinates:

https://rest.ensembl.org/overlap/region/arabidopsis_thaliana/4:13027892-13027892?feature=transcript&content-type=application/json

This returns 4 transcripts/cDNAs, including AT4G25510.1.

You can now map coords from that cDNA to the genomic space as follows:

https://rest.ensembl.org/map/cdna/AT4G25510.1/100..300?content-type=application/json

If this approach works for you you might want to check the tutorials and scripts at https://link.springer.com/protocol/10.1007/978-1-0716-2067-0_2