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Different fasta files

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

rna-seq
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written by sinha.puja • sinha.puja

1 answer

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

• 1 views • link
written by Kevin Blighe Kevin Blighe

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

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written by Ram Ram

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