Question: Analysis of Next Generation of Sequencing DAta
gravatar for Jerry Cholo
3.7 years ago by
Jerry Cholo170
Jerry Cholo170 wrote:


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.



ADD COMMENTlink modified 3.7 years ago by Sean Davis21k • written 3.7 years ago by Jerry Cholo170
gravatar for Sean Davis
3.7 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

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.

ADD COMMENTlink written 3.7 years ago by Sean Davis21k
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