How to retrieve all the possible RNA-seq data sets from public data bases?

Question

[Jaan]

Hi

I have a task which I have to collect every possible sets of RNA-seq data from a public database (GEO, ArrayExpress, etc) for Arabidopsis thaliana, and start to look for some analysis on them.

Meanwhile, I tried GEOquery and ArrayExpress packages in R, but what I get is a .soft file, which is a mixture of all NGS technologies like CHIP-seq and/or etc. as well.

Does anyone can help me to fetch all the possible data sets/experiments done by RNA-seq only!?

Thanks a lot

Answer 1

[Matt Shirley]

You want to query NCBI sequence read archive and not GEO. Many people make this mistake when looking for sequencing data. GEO hosts a subset of experiments that use sequencing technologies, but is still primarily a repository for array data. Even for GEO projects that have sequencing, then data are actually linked to from the SRA database. You can perform an advanced search like this one.

[Sean Davis]

One can use SRAdb package (or the accompanying SQLite database) to find such results using SQL queries.