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
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.
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written
by
Matt Shirley
One can use SRAdb package (or the accompanying SQLite database) to find such results using SQL queries.
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written
by
Sean Davis
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