In our RNA-seq pipeline we have a step after mapping that converts ensembl gene ID's (eg ENSMUSG00000096126) to gene names. When the pipeline was builded we mapped read files to older versions of the mouse genome.
What happens when new samples mapped on the newest version of the murine genome is run trough the pipeline? Will we just miss the gene names of the transcripts that were not included in the old built of the murine genome? Are there any additional consequences?
Thank you for your time,