Hello,

I want to ask a basic question. So, I read from the readme in the Ensembl ftp for Hg38 reference and it seems there are several type of file of dna, which is only dna, dna_sm, and dna_rm. If I want to align some fastq file to Ensembl, to which kind of file I should choose? I notice that I should merge all of the fasta file which is per chromosome based fasta into 1 single fasta file and then create index and then do the alignment process. Should I merge all of the file that I download from Ensembl or I should choose only what I need? If I need to choose, how to choose what I need based on my fastq. Thank you for your help and explanation. By the way, I already merge all of the fasta file into 1 single file (including the one with PATCH name in it) and currently I'm aligning my data.
The answer is to use the primary assembly. ftp://ftp.ensembl.org/pub/release-79/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz