Hello,

I would like to use publicly available datasets (next generation of sequencing including both DNA and RNA sequencing data) associated to “ovarian cancer” existing in Sequence Read Archive (SRA) or any other resources.

May someone let me know which package(s) is (are) available through Bioconductor allowing me to play with the software so that I can both EXTRACT and ANALYZE the data?

To extract the data, I used SRAdb, but I don’t know how to use “rs” (please see below)

rs = getSRA(search terms = "ovarian cancer", out types = c("run", "study"), sra con = sra con)

to analyze the data.  I appreciate if someone can provide me some information.

Thanks,

Jerry   

There might be a bit of confusion.  SRAdb allows quick and SQL-based searches of SRA metadata.  In some cases when the data are open-access and not controlled-access, SRAdb can facilitate downloading SRA data.  To perform searches, the getSRA function returns a data.frame (called "rs" in the question).  The function, getSRAfile() is used to actually get the data; read the help page for more details.  Once the data are downloaded, the SRA toolkit (a separate software package available from NCBI) to extract the data from the archive files downloaded from SRA.  Analysis will be up to you at that point and will often involve both bioconductor and non-bioconductor tools.