Entering edit mode
4.1 years ago
nikolai.markov
▴
10
Hello
I wonder if there's a way to get the information provided by http://useast.ensembl.org/Homo_sapiens/Tools/IDMapper programmatically, through biomaRt or some other software. Maybe this information is stored somewhere in ensembl ftp release?
Specifically, I have a list of human ensembl IDs for build 84 and for build 93, and I need to reconcile them.
Thank you, Jean-Karim. I read about Ensembl data schema yesterday and now better understand what I want: do you know if there is a way to convert build 84 ids into build 93 ids via stable id history records? Or, more generally, build X to build Y
The only easy option I know is this IDmapper.pl script. The alternative is to remap sequences associated with the old IDs (for example probe sequences) to the new build and get corresponding IDs and with mapping yourself, you can decide what to do in various cases.