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I proposed myself to replicate the results in this paper with an accession number PRJNA325650. So, I'm trying to download the data. Which will be the best way to do this?. I tried with the sratoolkit, and the SRAdb package in R but doesn't work.

My code:

In sratoolkit

Input:

prefetch PRJNA325650

Output:

prefetch.2.10.5 err: error unexpected while resolving query within virtual file system module - failed to resolve accession 'PRJNA325650' - The object is not available from your location. ( 406 )

In R (SRAdb)

Input:

rs = listSRAfile(c("PRJNA325650"), sra_con, fileType = 'sra')

Output:

Error in sraConvert(in_acc, out_type = c("study", "sample", "experiment",  : 
  Input type shuld be in 'SRA' 'ERA' 'DRA' 'SRP' 'ERP' 'DRP' 'SRS' 'ERS' 'DRS' 'SRX' 'ERX' 'DRX' 'SRR' 'ERR' 'DRR'

Any suggestions or methods?

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  • $\begingroup$ I’m voting to close this question because it is off-topic. In particular, this question has no biological component, but it might be suitable for migration to Bioinformatics. Please revisit the tour and read the help center for details. $\endgroup$ – tyersome May 15 at 15:08
  • $\begingroup$ Sorry, but the tags "bioinformatics" and "ncbi" are here and not in StackOverflow. $\endgroup$ – Adonis Cedeño May 15 at 15:18
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    $\begingroup$ The fact that there is a tag is irrelevant to whether a question is or is not on topic. That is set out in the Tour. People here are happy with bioinformatics questions where the biological problem is to the fore, but less so with questions on particular software or coding. In any case you are more likely to get an answer on SE Bioinformatics, so I would advise you to move your question there. $\endgroup$ – David May 15 at 15:46
  • $\begingroup$ Ok, I'm going to move it $\endgroup$ – Adonis Cedeño May 15 at 17:02
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I had a look, I can see the data in FASTA format. The accession number is for a project with 50 samples, each of them a sequencing run.

First I went to genbank at https://www.ncbi.nlm.nih.gov/

search that accession nunber selecting "all databases" to get the project page here https://www.ncbi.nlm.nih.gov/bioproject/325650

Under "resources" there is "sequence data" "SRA experiments"

to the right I clicked on the number 50, taking me to: https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=325650

I see the list of 50 samples, Clicking on the first I get to: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3667045

Clicking "Runs" takes me to a page with the data viewable in many forms. hope this helps.

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