Question: Differences between archived versions of ensembl
gravatar for Joe.waldron
10 days ago by
Joe.waldron0 wrote:

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

rna-seq alignment ensembl • 142 views
ADD COMMENTlink modified 9 days ago by Emily_Ensembl13k • written 10 days ago by Joe.waldron0
gravatar for Jean-Karim Heriche
10 days ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche13k wrote:

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.

ADD COMMENTlink written 10 days ago by Jean-Karim Heriche13k

OK thanks very much for your reply

ADD REPLYlink written 9 days ago by Joe.waldron0
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