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entrez_post and fetch do not return the same results #173

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JonathonMifsud opened this issue Aug 16, 2021 · 0 comments
Open

entrez_post and fetch do not return the same results #173

JonathonMifsud opened this issue Aug 16, 2021 · 0 comments

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@JonathonMifsud
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Hi,

I am trying to use rentrez to get the run info from a large number of SRA runs. I have worked out that I will need to use entrez_post to get a web_history object to use with entrez_fetch. However, I notice that the runinfo returned does not correspond to the SRA run provided.
Here is an example with a single SRA run (ERR1223411 ) which should link to a study titled “Identification of SNPs linked to putative resistance loci in the Dothistroma-Pinus pathosystem” however this is not the case:

wh <-
rentrez::entrez_post(
db = "sra",
id = "ERR1223411",
)

entrez_fetch(
db = "sra",
rettype =
"runinfo",
retmode =
"xml",
parsed = TRUE,
web_history = wh,
)

The SRA run output as part of the results is ERR718719

Any help would be greatly appreciated!

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