Answers.Body: <p>Download the ones without a chromosome number in the filename. Those files are the whole genome.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-21T13:49:30.357Z
Answers.Text: deleted my answer, this is much better
Answers.UserDisplayName: Pallie
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Answers.CreationDate: 2019-11-21T15:52:40.653Z
Answers.Text: 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?
Answers.UserDisplayName: Mark
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-21T16:19:39.050Z
Answers.Text: 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.
Answers.UserDisplayName: Emily_Ensembl
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-21T16:52:52.423Z
Answers.Text: 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!
Answers.UserDisplayName: Mark
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-22T13:01:44.470Z
Answers.Text: 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.
Answers.UserDisplayName: Emily_Ensembl
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-21T13:13:12.653Z
Answers.LastActivityDate: 2019-11-21T16:19:59.927Z
Answers.LastEditDate: 2019-11-21T16:19:59.927Z
Answers.UserDisplayName: Emily_Ensembl
Body: <p>I am trying to map a RNA-seq dataset using ensembl genome for medaka fish. </p>
  
  <p>From here <a href="http://uswest.ensembl.org/Oryzias_latipes/Info/Index" rel="nofollow noreferrer">http://uswest.ensembl.org/Oryzias_latipes/Info/Index</a></p>
  
  <p>when I click on a <code>Download DNA sequence (FASTA)</code> I am forwarded here <a href="ftp://ftp.ensembl.org/pub/release-98/fasta/oryzias_latipes/dna/" rel="nofollow noreferrer">ftp://ftp.ensembl.org/pub/release-98/fasta/oryzias_latipes/dna/</a></p>
  
  <p>where I have a huge number of <code>.fa.gz</code> files and I am just looking for a single file, that I can use. </p>
  
  <p>While when I am downloading medaka genome from NCBI (and using this technique) <a href="http://www.metagenomics.wiki/tools/fastq/ncbi-ftp-genome-download" rel="nofollow noreferrer">http://www.metagenomics.wiki/tools/fastq/ncbi-ftp-genome-download</a> I have my ncbi genome in one file.</p>
  
  <p>How can I get an ensembl genome in one file? </p>
  
Tags: <rna-seq><ensembl>
Title: Where can I get ensembl Medaka genome for RNAseq
ThreadText: # Where can I get ensembl Medaka genome for RNAseq
  
  (Asked by: username_0 on 2019-11-20)
  
  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?
  
  **Tags:** rna-seq, ensembl
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-11-21. Score: 3 | Accepted answer
  
  Download the ones without a chromosome number in the filename. Those files are the whole genome.
  
  > **Comments:**
  > **username_2**: deleted my answer, this is much better  
  > **username_0**: 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?  
  > **username_1**: 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.  
  > **username_0**: 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!  
  > **username_1**: 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.  
  
  ---
  
  