On Mar 4, 2011 11:15 AM, "kirti prakash" <kirtiprakash3.14@gmail.com> 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
>
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>
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