Difference between CellRanger reference genome and Ensembl/UCSC?

Question

[PianoEntropy]

What are the differences between the refence genomes provided by CellRanger and standard references such as those from Ensembl, or UCSC?

Basically, I made a custom reference with inserted RFP/YFP sequences from an Ensembl reference genome, and then applied cellranger to align 10x single-cell RNA-seq data to this genome (also repeated the alignment with STAR and more custom options). Is this OK, or should redo everything starting from the reference genome CellRanger provides?

[GenoMax]

I made a custom reference with inserted RFP/YFP sequences from an Ensembl reference

Did you use this procedure when building custom reference for use with cellranger?

10x uses Ensembl references so there should be no difference in genomes provided by them if you are using standard genomes.

[PianoEntropy]

Yeah, I followed the steps in your link. Good to know that they should be the same. Thanks!

[GenoMax]

Keep in mind that they are probably not building these genomes for each Ensembl release so while the sequence is unlikely to be different the annotation may not be the latest available from Ensembl. See this link for build procedure of standard genomes.