Hi Sean and Martin, Thanks a lot for the clarification.
Do you some other function now that converts SRA to fastq format ? I wonder how much space NCBI saves by deleting fastq files and what is extra advantage of having of SRA files. Kirti On Fri, Mar 4, 2011 at 9:23 PM, Martin Morgan <[email protected]> wrote: > On 03/04/2011 10:10 AM, Sean Davis wrote: > > On Mar 4, 2011 11:15 AM, "kirti prakash" <[email protected]> > wrote: > >> > >> Hi, > >> > >> I wanted to get fastq files associated with some SRA > >> > >> So I was going through the following SRAdb vignettes > >> > > > http://bioconductor.org/packages/2.6/bioc/vignettes/SRAdb/inst/doc/SRAdb.pdf > >> > >> < > > > http://bioconductor.org/packages/2.6/bioc/vignettes/SRAdb/inst/doc/SRAdb.pdf > >> I > >> am able to run most of the commands except the ones in section 3.5(which > I > >> actually need) > >> > >> The error I am getting is > >> getFastq (in_acc=c("SRR000648","SRR000657"), sra_con=sra_con, > >> destdir=getwd()) > >> Error: could not find function "getFastq" > >> > >> getFastq > >> Error: object 'getFastq' not found > >> > >> Similarly for listFastq and getFastInfo functions > >> > >> I am wondering if I am missing something ? > > > > Unfortunately, you are not. NCBI has removed the fastq files from its > site, > > so these functions have been removed from sraDB. > > Also, I think your version of R and SRAdb don't match (biocLite > installed SRAdb version 1.2.1 under R-2.11.1). A better bet is to update > to R-2.12.2, update your installed packages > > http://bioconductor.org/install/ > > and use the current vignette, available with > > browseVignettes("SRAdb") > > This won't make getFastq magically appear, but it will make the software > and vignette function in a consistent way. > > Martin > > > > > Sean > > > >> Best regards, > >> > >> Kirti Prakash > >> > >> sessionInfo() > >> R version 2.11.1 (2010-05-31) > >> x86_64-unknown-linux-gnu > >> > >> locale: > >> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C > >> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 > >> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915 > >> [7] LC_PAPER=en_US.iso885915 LC_NAME=C > >> [9] LC_ADDRESS=C LC_TELEPHONE=C > >> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] SRAdb_1.4.1 graph_1.28.0 RSQLite_0.9-2 DBI_0.2-5 > >> > >> loaded via a namespace (and not attached): > >> [1] Biobase_2.8.0 GEOquery_2.16.3 RCurl_1.4-3 tools_2.11.1 > >> [5] XML_3.1-0 > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> Bioc-sig-sequencing mailing list > >> [email protected] > >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
