When you look at all the genome files available from Ensembl. You are presented with a bunch of options. Which one is the best to use/download?You have a combination of choices.First part options:dna_sm - Repeats soft-masked (converts repeat nucleotides to lowercase)dna_rm - Repeats masked (converts repeats to to N's)dna - No maskingSecond part options:.toplevel - Includes haplotype information (not sure how aligners deal with this).primary_assembly - Single reference base per positionRight now I usually use a non-masked primary assembly for analysis, so in the case of humans:Homo_sapiens.GRCh38.dna.primary_assembly.fa.gzDoes this make sense for standard RNA-Seq, ChIP-Seq, ATAC-Seq, CLIP-Seq, scRNA-Seq, etc... ?In what cases would I prefer other genomes? Which tools/aligners take into account softmasked repeat regions?
What Ensembl genome version should I use for alignments? (e.g. toplevel.fa vs. primary_assembly.fa)
fasta;genome;ensembl;biomart