Question: DEG by Trinity pipeline
gravatar for mina
4.2 years ago by
mina20 wrote:


I have 3 samples RNA-seq   and I want to do Differential expression for each sample. These are the following step that my supervisor want me to do. 

""1. Merge assembly using all RNA-seq data - blast the merged assembly for annotation, first using uniprot, then nr database

2. Perform read counting of individual RNA-seq data against the merge assembly 

3. Perform correlation analysis between your biological replicates (sample 1, 2 & 3)

You have to keep the result tables from each step of your analysis. I suggest you use the Trinity pipeline for merge assembly and annotation.""

I did merging using "cat "  and assembly by "" command line and also blast (blastp). but I don know how to do step 2 and 3.

Hope anyone can help me to proceed with this step.

English is not my first language, so please excuse any mistakes.

Thanks in forward.


deg rna-seq trinity • 1.4k views
ADD COMMENTlink modified 4.2 years ago by biogirl160 • written 4.2 years ago by mina20
gravatar for biogirl
4.2 years ago by
European Union
biogirl160 wrote:

The paper by Brian Haas et al. (link here) has a really good step-by-step pipeline for analysing RNAseq reads with Trinity, including DEG analysis.

ADD COMMENTlink written 4.2 years ago by biogirl160
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