unclear which genomic fasta to use

[yfarjoun]

in ensembl there are 3 different "top-level" genomic fastas (for human atleast):

unmasked, hard-masked and soft-masked:

I presume that these will result in different indexes and thus different pseudo alignments and results. Could you clarify which "flavor" of genomic fasta will be most appropriate for creating an index with?

[Yenaled]

I don't use masked genomes. I use the unmasked Ensembl genome or the GENCODE genome.

Also see https://kb.10xgenomics.com/hc/en-us/articles/360060307872-Does-my-genome-sequence-needs-be-masked-or-unmasked-for-custom-reference-generation-

[yfarjoun]

thanks.