Answers.Body: <p>I strongly recommend switching to SRA <a href="https://www.ncbi.nlm.nih.gov/sra" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/sra</a></p>
  <p>Whether the following would work ...</p>
  <pre><code>esearch -db sra -query &quot;{species name }&quot; | esummary
  </code></pre>
  <p>I'm not at all sure because SRA has its own toolkit. Maybe NCBI <code>e-utilities</code> <code>e-summary</code> <code>efetch</code> would work on the SRA database. However, the weblink certainly works for transcriptomics.</p>
  <p>NCBI has shifted some of its database to be housed off-site onto GCP and AWS and I have a feeling these may not be accessible to <code>e-utilities</code>, but I could be wrong.</p>
  <p>Just to note, what I envisage the question meaning is a complete transcriptomic study for a given species (or given sample) under given experimental conditions.</p>
  <hr />
  <p>Comments. I better clarify, SRA will be raw Illumina output, it is not assembled into exome cDNA. <code>e-utils</code> is basically for assembled cDNA, it might give you the information - I really don't think it will download it though. So to answer your questions, yes the data will be there on SRA, whether this is the format you want is a different question.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-16T21:36:30.440Z
Answers.Text: I am actually looking for RNA-seq data for the whole exome. I will try to see if I can find transcriptions and cDNA using SRA. Hopefully off-housing has not affected the API.
Answers.UserDisplayName: Sudoh
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-16T22:18:12.153Z
Answers.Text: @Sudoh Exome, that would be assumed .... there's a format issue. Post-updated
Answers.UserDisplayName: M__
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Answers.CreationDate: 2023-01-16T20:54:27.110Z
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Answers.LastEditDate: 2023-01-16T22:21:19.213Z
Answers.UserDisplayName: M__
Body: <p>How to find specific types of assemblies for specific species using entrez tools?</p>
  <p>Task: Trying to specifically find transcriptomes and associated cDNA data for a list of speices.</p>
  <p>I can use this oneliner <code>esearch -db assembly -query &quot;{species name }&quot; | esummary</code> to get a list of assemblies and associated data available for any given species.</p>
  <p>I can use <code>esearch -db assembly -query &quot;{species name }&quot; | xtract -pattern ENTREZ_DIRECT -element Count</code> to find any specific info nested within the XML tree.</p>
  <p>Now I am not sure how to find if the assembly is a transcriptome (which is what I am looking for). I have tried to <code>CRTL +f</code> terms like <code>rna</code>, <code>peptide</code>,<code>amino acids</code> to no avail and I guess there is a chance I am missing something while looking it over manually.</p>
  <p>For example here is the output for <a href="https://www.pastery.net/atxtjn/" rel="nofollow noreferrer">&quot;zea mays&quot;</a>.</p>
  <p>Does anyone have any clues? Or should I be using a different db or different tool?</p>
  
Tags: <assembly><transcriptome><entrez>
Title: How to find specific types of assemblies for specific species using entrez tools?
ThreadText: # How to find specific types of assemblies for specific species using entrez tools?
  
  (Asked by: username_0 on 2023-01-16)
  
  How to find specific types of assemblies for specific species using entrez tools?
  
  Task: Trying to specifically find transcriptomes and associated cDNA data for a list of speices.
  
  I can use this oneliner `esearch -db assembly -query "{species name }" | esummary` to get a list of assemblies and associated data available for any given species.
  
  I can use `esearch -db assembly -query "{species name }" | xtract -pattern ENTREZ_DIRECT -element Count` to find any specific info nested within the XML tree.
  
  Now I am not sure how to find if the assembly is a transcriptome (which is what I am looking for). I have tried to `CRTL +f` terms like `rna`, `peptide`,`amino acids` to no avail and I guess there is a chance I am missing something while looking it over manually.
  
  For example here is the output for ["zea mays"](https://www.pastery.net/atxtjn/).
  
  Does anyone have any clues? Or should I be using a different db or different tool?
  
  **Tags:** assembly, transcriptome, entrez
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-01-16. Score: 0 | Accepted answer
  
  I strongly recommend switching to SRA <https://www.ncbi.nlm.nih.gov/sra>
  
  Whether the following would work ...
  
  ```
  esearch -db sra -query "{species name }" | esummary
  
  ```
  
  I'm not at all sure because SRA has its own toolkit. Maybe NCBI `e-utilities` `e-summary` `efetch` would work on the SRA database. However, the weblink certainly works for transcriptomics.
  
  NCBI has shifted some of its database to be housed off-site onto GCP and AWS and I have a feeling these may not be accessible to `e-utilities`, but I could be wrong.
  
  Just to note, what I envisage the question meaning is a complete transcriptomic study for a given species (or given sample) under given experimental conditions.
  
  ---
  
  Comments. I better clarify, SRA will be raw Illumina output, it is not assembled into exome cDNA. `e-utils` is basically for assembled cDNA, it might give you the information - I really don't think it will download it though. So to answer your questions, yes the data will be there on SRA, whether this is the format you want is a different question.
  
  > **Comments:**
  > **username_0**: I am actually looking for RNA-seq data for the whole exome. I will try to see if I can find transcriptions and cDNA using SRA. Hopefully off-housing has not affected the API.  
  > **username_1**: @username_0 Exome, that would be assumed .... there's a format issue. Post-updated  
  
  ---
  
  