On Wed, Jan 5, 2011 at 7:47 AM, Mark Dunning <firstname.lastname@example.org>
> Hi Sean,
> That's a shame. Thanks for the information. I think I can get the
> fastqs I need by another means though.
You don't have to work too hard at it. The process is described here:
In short, you'll need the SRA SDK to do so.
Binaries are available for several architectures and OSes.
> On Wed, Jan 5, 2011 at 11:54 AM, Sean Davis <email@example.com>
> > On Wed, Jan 5, 2011 at 6:29 AM, Mark Dunning
> >> Hi,
> >> I am hoping to download some Fastq files from the Short Read
> >> and am following the vignette for SRAdb. However, I get an error
> >> trying the example of using listFastq
> >> > listFastq("SRA011804", sra_con = sra_con)
> >> Error in curlPerform(curl = curl, .opts = opts, .encoding =
> >> Server denied you to change to the given directory
> > Hi, Mark. Unfortunately, we are going to have to remove fastq
> > as NCBI has removed the fastq files:
> > We are looking at workarounds for this, but for the time being,
> > functionality is broken and will not likely be retained in the
> > Sean
> >> I think I have setup the sra_con object correctly
> >> > sra_con
> >> <sqliteconnection: dbi="" con="" (2626,="" 2)="">
> >> > dbListFields(sra_con, "study")
> >>  "study_ID" "study_alias"
> >>  "study_title" "study_type"
> >>  "center_name" "center_project_name" "project_id"
> >>  "study_description" "study_url_link"
> >>  "study_attribute" "submission_accession"
> >> >
> >> Cheers,
> >> Mark
> >> > sessionInfo()
> >> R version 2.12.0 (2010-10-15)
> >> Platform: x86_64-pc-linux-gnu (64-bit)
> >> locale:
> >>  LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
> >>  LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
> >>  LC_MONETARY=C LC_MESSAGES=en_GB.utf8
> >>  LC_PAPER=en_GB.utf8 LC_NAME=C
> >>  LC_ADDRESS=C LC_TELEPHONE=C
> >>  LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
> >> attached base packages:
> >>  stats graphics grDevices utils datasets methods
> >> other attached packages:
> >>  SRAdb_1.4.0 graph_1.28.0 RSQLite_0.9-3 DBI_0.2-5
> >> loaded via a namespace (and not attached):
> >>  Biobase_2.10.0 GEOquery_2.16.3 RCurl_1.4-3 tools_2.12.0
> >>  XML_3.2-0
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
[[alternative HTML version deleted]]