I am trying to design a pipeline to study the differential gene expression in human embryonic stem cells during its various stages of development and with adult cells. The primary source of data will be NCBI-SRA.
A basic workflow that I have in mind I based on the RNA-seq tutorial from Griffith Lab (https://github.com/griffithlab/rnaseq_tutorial/wiki).
I need a few help in finalising the work.
- What are the primary things to be considered while downloading my data?
- Do all experiments use ERCC spike-in for quality control?
- For alignment of reads of Reference Genome is a simple HP desktop with 8gb RAM sufficient? Or do I need to upgrade?