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?
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.