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. 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
