Does anyone know how much difference there is between each version of the ensembl transcriptome? Our collaborator has recently analysed some RNA-seq data for us but he mapped to ensemble 75 for this. This is from Feb 2014 and part of GRCh37. Does anyone know if this is an issue or if it would be almost exactly the same as the most recent version? Many thanks
One of the major differences between versions is the underlying assembly. Version 75 is the last one on GRCh37, from version 76 on, the assembly is GRCh38. The GRCh37 version of Ensembl is regularly updated (at least for the time being) so using GRCh37 shouldn't be an issue as long as you make sure you use data that refers to this assembly. For example, don't use Ensembl genes defined on GRCh38. Some of them or some of their transcripts may not be represented on GRCh37. Also the status/type of some genes may be different. In the end whether it matters or not depends on what you're going to use the assembly and its annotations for. For example, GRCh38 has closed gaps existing in GRCh37.