I recently did RNASeq and have the Paired-end read, I have checked quality in FastQC and trimmed the ends with Trimmomatic. Does any one have a pipeline I could use to do downstream analysis. I have been learning online/youtube etc. No formal training on these kind of analysis. I am interested in differential expression profiles (compare Control and Treatment), and identify unique genes expressed at different stages on my treatment.
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written
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Nattoh Godfrey •
1 answer
For an overview the different ways to analyze your data you can refere to this.
With regards to gene DE analysis there are two major ways you can go:
Option 1) I just want to get this done asap. There are many possibilities but you can use a tool like 3D RNA-seq or Galaxy
Option 2) I want to learn some bioinformatics and R coding along the way: Again there are many options but a good place to start is this workflow using DESeq2 which have links to the other things you need.
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