Get data from SRA with just SAMN IDs
0
1
Entering edit mode
2.5 years ago
mark.dunning ▴ 230

Hi,

We have student that would like to analyse and RNA-seq data for a project. According to the publication, the fastq files are open access and available

https://pubmed.ncbi.nlm.nih.gov/28511992/

However, the only IDs I can find are "SAMN".

https://www.ncbi.nlm.nih.gov/biosample?Db=biosample&DbFrom=bioproject&Cmd=Link&LinkName=bioproject_biosample&LinkReadableName=BioSample&ordinalpos=1&IdsFromResult=347568

I'm familiar with sra-toolkit, but to use that I need the SRR IDs. Does anyone know how I can find these IDs for this dataset?

Regards,

Mark

SRA NCBI RNA-Seq fastq • 903 views
ADD COMMENT
0
Entering edit mode

Hmm, I do not see any references to the actual sequencing data at SRA, nor any relevant entries for the bioproject when querying ENA or sra-explorer.info

Maybe your best chance is to contact the authors.

ADD REPLY
0
Entering edit mode

Hi Mark, were you able to get this to work? I am facing the same issue

ADD REPLY

Login before adding your answer.

Traffic: 909 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6