Question: the difference of RNA-seq data between GEO data and raw data
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gravatar for 78956287
4.1 years ago by
789562870
789562870 wrote:

 I want to analyse the RNA-seq (eg GSE50676, Illumina HiSeq 2000). But I don't know the difference between GEO data (GSE50676_RAW.tar) and the raw data (SRR972706.sra). How have you transferred the raw data to the GEO data? How should I begin if I want to analyse the GEO data?

rna-seq R • 2.0k views
ADD COMMENTlink modified 4.1 years ago by Devon Ryan90k • written 4.1 years ago by 789562870
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gravatar for Sean Davis
4.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

The GSE50676_RAW.tar is an archive file containing tab-delimited text files.  As you probably know, tab-delimited text files are only useful if you know what is in them.  So, you may have to download the file and look in it to see if there is something useful to you.  

The SRA link will be to the actually reads which you could download and then use to reproduce an analysis de novo.  

As to your final question, as to how to begin to analyze GEO data, that will depend entirely on what questions you have and what data are available.  

ADD COMMENTlink written 4.1 years ago by Sean Davis25k
0
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

You'll want to use the file from SRA (SRR972706.sra) with fastq-dump. The .tar file seems to contain unfiltered analyses.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by Devon Ryan90k
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