I have a log2RPKM counts data that I want to analyze to find differentialy expressed genes from this data, In my case I am trying to analyze data from the GEO102741 dataset which has both control and subjects data
My questions are following
1) The data given is log2RPKM counts data so do I need to convert these counts to some other format using some technique, is there some free online tool that I can use to convert this data to some format that is required for Gene Expressions
2) How can I find DEGs(Deferentially Expressed Genes) From this dataset , is there some online state of the art tool for free that I can use to find DEGs
I am new to this DEGs and RNASeq datasset domain so I apologize if this question is too naive.
What is my GOAL?
My end goal is that I want to perform clustering of genes in the dataset in both control and autism separately and want to see how many clusters perform and will then dig deeper , for these clusters like how the clusters vary in size in two groups and then I will use DEGs genes and also cluster them and this time I will compare them across different datasets that is in different datasets I will perform these kind of operations and will compare DEGs across datasets.Please if somebody has some useful suggestions then please guide me.
At the this link a huge SRA dataset is available but downloading and running the suggested software on data is not possible for me due to limited bandwidth, lack of storage and lack of computational power.