How to search by instrument in SRA?

[Jasmine]

Hello all,

I'm looking for a public data set which used Genome Analyzer IIx. Does anyone know how to search NCBI SRA site by instrument name?

I'd like to find a data set which use 100bp read.

Thanks!
Jasmine

[aaronh]

With a little bit of R and SQL, you can find whatever you want using the SRAdb package. http://www.bioconductor.org/packages...tml/SRAdb.html

[Jasmine]

Thank you, this is fantastic. I'll take a look at the package.

[Jasmine]

I could find the Illumina Genome Analyzer IIx data by below steps using SRAdb package I thought I should share what I did.

source("http://bioconductor.org/biocLite.R")
biocLite("SRAdb")
library(SRAdb)

# Get SRA db file
sqlfile <- getSRAdbFile()

sra_con <- dbConnect(SQLite(), sqlfile)

# Search by Illumina Genome Analyzer IIx
rs = getSRA(search_term="Illumina Genome Analyzer IIx",sra_con=sra_con)

# This gives the SRA number.
rs[,"experiment"]

More information is here http://bioconductor.org/packages/2.6.../doc/SRAdb.pdf.