Are reference sequences from GENCODE, Ensembl and RefSeq the same if they are called GRCh38.p10, it is just the annotation that varies?

Question

[amina.mcdiarmid]

I am looking to compare reference sequences and annotations (.gtf/.gff) to find a best fit for my analysis with regards to mapping. Aligners ask for a reference sequence in .fasta format with an annotation in .gtf or .gff format. Am I correct in assuming that it doesn't matter which data base you download the .fasta file because they are the same (provided they are all e.g. GRCh38.p10) and it is just the annotations which are produced differently? Or does each data base also have it's own reference sequences.

I think they contain the same information but are formatted so they match the .gtf files. Am I right? Help!

Answer 1

[GenoMax]

While the reference sequence is identical the identifiers may be different (e.g. chr1 for UCSC instead of 1 for Ensembl). This can mess things up if you mix and match sequence/annotation from UCSC/Ensembl.

.p10 is the patch version. Patches never change chromosomal coordinates so keep that in mind.