I am trying to map a RNA-seq dataset using ensembl genome for medaka fish.

From here http://uswest.ensembl.org/Oryzias_latipes/Info/Index

when I click on a Download DNA sequence (FASTA) I am forwarded here ftp://ftp.ensembl.org/pub/release-98/fasta/oryzias_latipes/dna/

where I have a huge number of .fa.gz files and I am just looking for a single file, that I can use.

While when I am downloading medaka genome from NCBI (and using this technique) http://www.metagenomics.wiki/tools/fastq/ncbi-ftp-genome-download I have my ncbi genome in one file.

How can I get an ensembl genome in one file?


1 Answer 1


Download the ones without a chromosome number in the filename. Those files are the whole genome.

  • $\begingroup$ deleted my answer, this is much better $\endgroup$
    – Pallie
    Nov 21, 2019 at 13:49
  • $\begingroup$ Thank you Emily, but is that link located on a same page?? I mean the one " without a chromosome number in"? And you said oneS - there are multiple medaka genomes? $\endgroup$
    – Mark
    Nov 21, 2019 at 15:52
  • $\begingroup$ Yes, they're all listed in the same folder. Check the README to see what you want in terms of toplevel, repeat masking etc, but they're all there. $\endgroup$ Nov 21, 2019 at 16:19
  • $\begingroup$ Thank you, but still... what I see is for example Oryzias_latipes.ASM223467v1.dna.primary_assembly.1.fa.gz Oryzias_latipes.ASM223467v1.dna_rm.primary_assembly.1.fa.gz Oryzias_latipes.ASM223467v1.dna_sm.primary_assembly.1.fa.gz but I cannot find something like Oryzias_latipes.ASM223467v1.fa.gz Sorry I am really new to bioinformatics and lots of things are new to me while they are somewhat obvious for the experts.. Thank you! $\endgroup$
    – Mark
    Nov 21, 2019 at 16:52
  • $\begingroup$ rm and sm refer to the repeat masking. rm is full repeat masking, all the repeats are replaced by Ns. sm is soft-masking, the repeats are in lower case. The other file has no repeat masking. $\endgroup$ Nov 22, 2019 at 13:01

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