Could anyone let me know which FASTA files that can be used to build genome index for analysis using STAR. 1- In Ensemble there is 10 unmasked fasta files (chromosomes 2L, 2R, 3L, 3R, 4, X, Y, nochromosomal, mitochondrion genome, and toplevel) ftp://ftp.ensembl.org/pub/release-92/fasta/drosophila_melanogaster/dna/. Which files should be included? Or is the dna_index the one that should be used ftp://ftp.ensembl.org/pub/release-92/fasta/drosophila_melanogaster/dna_index/
2- In flybase, there are also several fasta files, ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.21_FB2018_02/fasta/ Which files should be used for building genome index using STAR for mapping reads?