This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Download and explore data from bioproject

I want to be able to download / explore data available for https://www.ncbi.nlm.nih.gov/bioproject?LinkName=biosample_bioproject&from_uid=10846776

This bioproject consists of : Data Type Raw sequence reads - therefore the fles will be in fasta format.

There are two biosamples present and their landing page leads to https://www.ncbi.nlm.nih.gov/biosample/10846776

How can I download these biosamples via webpage / ftp server / programmatically.

I tried the [e-utilities][3] but did not succeed. These commands did not work for me.

efetch -db biosample -id 10846776 -format fasta
esearch -db bioproject -query 517829 |elink -target nuccore | efetch -format fasta

Thanks in advance for your help.

bioproject eutilities
• 2,304 views • link
updated by Ram Ram • written by club16 • club16

I appreciate the responses. Thanks.

• 0 views • link
written by club16 • club16

I am experiencing the same problems with handful of bioprojects I am unable to find the SRR number in the website itself. PRJNA232651 PRJNA756149 PRJNA778915 PRJNA778858 PRJNA232651

• 0 views • link
written by dhiraj16 • dhiraj16

I checked a couple of these accessions and it appears that these are assembly only submissions i.e. the raw data does not appear to have been submitted.

• 0 views • link
written by GenoMax GenoMax

2 answers

There is something odd about this submission. It appears that these samples either were not submitted to SRA or the link to the samples in SRA is broken. I suggest that you write to SRA help desk and ask.

• 0 views • link
written by GenoMax GenoMax

Obtaining the data programmatically should normally be possible using e.g. sra-tools or even more conveniently nf-core fetchngs.

However, I think the root cause of your problem is an issue with the original data submission. Normally, the SRA Run Selector should return a list of run accessions (starting with SRR...) for the corresponding BioProject ID, which however isn't the case for the given accession PRJNA517829.

Therefore, I'd suggest to reach out to the corresponding author and inquire regarding the data directly.

• 0 views • link
written by Matthias Zepper Matthias Zepper

Log in to answer this question.

More posts like this