Question: Where and how to fetch phenotype data of the relevant SRA-identified tuberculosis WGS samples?
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gravatar for bioinform
20 months ago by
bioinform20
bioinform20 wrote:

Where and how to fetch phenotype data of the relevant SRA-identified tuberculosis WGS samples? I am developing GWAS-based software, want to fetch pehnotype data from web, all the relevant available information to the fastqs I have. Is that information available for a single WGS sample and in what format it is?

gwas association sra software • 736 views
ADD COMMENTlink modified 20 months ago by Istvan Albert ♦♦ 80k • written 20 months ago by bioinform20

What kind of phenotypes are you looking for? Why only for one organism?

ADD REPLYlink written 20 months ago by Michael Dondrup46k

Hello bioinform/vassialk!

We believe that this post does not fit the main topic of this site.

Not a real question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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ADD REPLYlink modified 20 months ago • written 20 months ago by Michael Dondrup46k

How is fetching phenotype data not bioinformatics? It is one most important tasks (yet annoyingly difficult) that one needs to perform when attempting to reproduce results from papers. Alas the information (if available) is hidden away inside XML files (as my examples shows).

In addition, answers should not be closed when an answer has been submitted.

ADD REPLYlink written 20 months ago by Istvan Albert ♦♦ 80k

This is a bot question, I have always flagged them like that. It is most likely the vassialk bot again. Look at the similar questions, and the post history of this user. I don't want to deal with automatic users or invest more effort.

ADD REPLYlink modified 20 months ago • written 20 months ago by Michael Dondrup46k

Ok that makes sense and it warrants the closure - but you should state it more clearly that you believe this to be a bot.

ADD REPLYlink written 20 months ago by Istvan Albert ♦♦ 80k
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gravatar for Istvan Albert
20 months ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

You can get the public summary as an XML document though when it comes to clinical data phenotype information may be limited (not publicly available).

 # This will take a while
 esearch -query PRJNA46337 -db sra | efetch --format summary > summary.xml
 # Extract information
 cat summary.xml | xtract -pattern "EXPERIMENT_PACKAGE" -element PRIMARY_ID, TITLE | cut -f 8,10 | tail

will produce :

SRR1614838  Human metagenome DNA sample from stool of a female participant in the dbGaP study "The Neonatal Microbiome and NEC"
SRR1614836  Human metagenome DNA sample from stool of a male participant in the dbGaP study "The Neonatal Microbiome and NEC"
SRR1614835  Human metagenome DNA sample from stool of a female participant in the dbGaP study "The Neonatal Microbiome and NEC"
SRR1614833  Human metagenome DNA sample from stool of a male participant in the dbGaP study "The Neonatal Microbiome and NEC"
SRR1614832  Human metagenome DNA sample from stool of a female participant in the dbGaP study "The Neonatal Microbiome and NEC"
SRR1614830  Human metagenome DNA sample from stool of a female participant in the dbGaP study "The Neonatal Microbiome and NEC"
ADD COMMENTlink written 20 months ago by Istvan Albert ♦♦ 80k

I don't think SRA requires phenotypic data with all submissions, correct? bioinform : This will only work if the original submitters have provided this data.

ADD REPLYlink written 20 months ago by genomax65k
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