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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.

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.

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.

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Source Link
M__
  • 13k
  • 5
  • 29
  • 46

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.

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 under given experimental conditions.

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.

Source Link
M__
  • 13k
  • 5
  • 29
  • 46

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 under given experimental conditions.