Forum: Learning RNASeq Analysis using my own DATA that needs to be analyzed
0
gravatar for Nattoh Godfrey
5 weeks ago by
Nairobi
Nattoh Godfrey0 wrote:

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.

ADD COMMENTlink modified 5 weeks ago by kristoffer.vittingseerup3.0k • written 5 weeks ago by Nattoh Godfrey0

Try reproducing griffith lab tutorial on RNAseq (https://github.com/griffithlab/rnaseq_tutorial)

ADD REPLYlink written 5 weeks ago by cpad011212k
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gravatar for kristoffer.vittingseerup
5 weeks ago by
European Union
kristoffer.vittingseerup3.0k wrote:

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.

ADD COMMENTlink written 5 weeks ago by kristoffer.vittingseerup3.0k
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