Can anyone suggest me the recent and best pipeline for RNA-Seq data analysis

Question

[harshraje19]

Can anyone suggest me the recent and best pipeline for RNA-Seq data analysis. Specially for plants

[Shicheng Guo]

STAR: ultrafast universal RNA-seq aligner

https://github.com/alexdobin/STAR

https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf

[Kevin Blighe]

To help, please edit your post to explain in greater detail the experiment that you are planning to perform, and the ultimate goal(s) of this experiment.

[swbarnes2]

You should figure that people answering will not want to put in more than half the effort answering that you demonstrated you put in already. How much effort do you think you've demonstrated so far?

[cpad0112]

De novo or reference based?

Answer 1

[dsull]

As the comments above say, please give more detail about your experiments and the goals.

Here's a very minimal example: "I received RNA-seq results from Arabidopsis thaliana samples; I'm interested in doing differential gene expression analysis to see which genes significantly change in expression between my treatment samples and my control samples.".

In such a case, I would recommend a pipeline like: STAR -> DESeq2 (as Shicheng Guo's answer suggested). Alternatively, another good pipeline would be: kallisto -> sleuth

I would then suggest you to read up on the documentations on the programs in one of those pipelines to figure out how to use those programs. For differential gene expression analysis, there are many other pipelines that are good but the ones I suggested above work perfectly fine.