Question: Getting RNA-seq Data From ENA (or GEO/SRA)
gravatar for jiwpark00
3.0 years ago by
jiwpark00200 wrote:

If I want to get multiple RNA-seq FASTQ files from repositories (ENA or GEO, etc), what is the best way to go about this?

So far, what I do is, I find a paper, look at the GEO #, go to GEO page and get BioProject #, go to ENA, and then download the files. And essentially, if I wanted to do this for 5 papers, I would have to repeat the steps x5.

I have a list of genes that I'm interested in, and want to know how they have changed in RNA-seq profiles to determine how they change (before I decide whether or not doing my RNA-seq may be worthwhile). I know there are repositories that clump large # of data sets together but I want to know how to do it myself since I may only want to look at selected sets of RNA-seq (ie top 10 data sets most relevant to my experiments).

Thank you.

python rna-seq web R • 1.2k views
ADD COMMENTlink modified 5 months ago by ATpoint23k • written 3.0 years ago by jiwpark00200

ENA may be best since you don't need to deal with SRAtoolkit and can directly download fastq format files. But if you are familiar with SRAtoolkit then by all means go with SRA.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax71k

I heard of SRAtoolkit. Is it command-line friendly also?

I saw in literature people using SRAdb (R) to pull say, platform-specific RNA-seq files. But I'm not sure if that's better than SRAtoolkit or whether SRAdb (or any R package) let you pull RNA-seq file specific to your experiments of interest.

ADD REPLYlink written 3.0 years ago by jiwpark00200
gravatar for ATpoint
5 months ago by
ATpoint23k wrote:

Fast download of FASTQ files from the European Nucleotide Archive (ENA)

ADD COMMENTlink written 5 months ago by ATpoint23k
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