I recently started some RNAsequencing of tumor samples. My main question is regarding the differential gene expression among samples and controls. I have successful utilized tophat, cufflinks, and cuffdiff. I am new to bioinformatics and RNAseq analysis. My experience utilizing Linux terminals for analysis is only recent. I have seen a few tutorials online for RNAseq, but some of them only take you through the cufflinks data retrieval. I am looking for what next....the steps and analysis after cuffdiff. Are there programs that exist or tutorials that exist for running a script in python or R for analysis of the data? How do others go about analyzing RNAseq data for differential expression among samples?
Any advice on the downstream analysis of RNAseq data after the tuxedo suite would be greatly appreciated.
Thanks!
Any advice on the downstream analysis of RNAseq data after the tuxedo suite would be greatly appreciated.
Thanks!
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