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",
)
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!