<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>

CC BY-SA 4.0
2023-01-16T21:36:30.440Z
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.
Sudoh
CC BY-SA 4.0
2023-01-16T22:18:12.153Z
@Sudoh Exome, that would be assumed .... there's a format issue. Post-updated
M__
CC BY-SA 4.0
2023-01-16T20:54:27.110Z
2023-01-16T22:21:19.213Z
2023-01-16T22:21:19.213Z
M__
<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>

<assembly><transcriptome><entrez>
How to find specific types of assemblies for specific species using entrez tools?
# 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

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## 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**: @Sudoh Exome, that would be assumed .... there's a format issue. Post-updated  

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