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".

Does anyone have any clues? Or should I be using a different db or different tool?


1 Answer 1


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.

  • $\begingroup$ 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. $\endgroup$
    – Sudoh
    Jan 16, 2023 at 21:36
  • $\begingroup$ @Sudoh Exome, that would be assumed .... there's a format issue. Post-updated $\endgroup$
    – M__
    Jan 16, 2023 at 22:18

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