Question: How to retrieve all the possible RNA-seq data sets from public data bases?
gravatar for Jaan
6.0 years ago by
Jaan0 wrote:


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.

Mean while, 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 alot


sequencing rna-seq next-gen R • 4.5k views
ADD COMMENTlink modified 6.0 years ago by Matt Shirley9.3k • written 6.0 years ago by Jaan0
gravatar for Matt Shirley
6.0 years ago by
Matt Shirley9.3k
Cambridge, MA
Matt Shirley9.3k wrote:

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

ADD COMMENTlink written 6.0 years ago by Matt Shirley9.3k

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

ADD REPLYlink written 6.0 years ago by Sean Davis26k
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