Different fasta files

Question

[sinha.puja]

Can anyone tell me what is the difference between between three files shown below:

Homo_sapiens.GRCh38.dna.toplevel.fa.gz

Homo_sapiens.GRCh38.dna_rm.toplevel.fa.gz

Homo_sapiens.GRCh38.dna_sm.toplevel.fa.gz

Answer 1

[Kevin Blighe]

The information is in the README: ftp://ftp.ensembl.org/pub/release-93/fasta/homo_sapiens/dna/README

sequence type:

• 'dna' - unmasked genomic DNA sequences.

  • 'dna_rm' - masked genomic DNA. Interspersed repeats and low complexity regions are detected with the RepeatMasker tool and masked by replacing repeats with 'N's.

  • 'dna_sm' - soft-masked genomic DNA. All repeats and low complexity regions have been replaced with lowercased versions of their nucleic base

[Ram]

One could even google dna_rm and check out the first link in the results.