DEG by Trinity pipeline

Question

[mina]

Hello

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 Trinity.pl 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

Regards

Answer 1

[biogirl]

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.