CUFFLINKS FROM TOPHAT2 STUFF...

Question

[revenge.com]

I know Tophap2 is used with Bowtie2 for genome alignment and reference, but what does cufflinks do specifically?

Answer 1

[dsull]

Cufflinks assembles the aligned reads into transcripts so that you can get the expression levels of the transcripts (e.g. in FPKM units).

Here's a paper: https://www.nature.com/articles/nprot.2012.016 And here's an overview of the workflow: http://cole-trapnell-lab.github.io/cufflinks/manual/

Note that Tophat2/Cufflinks is no longer one of the best-practices workflows for RNA-seq analysis. Might I suggest upgrading to kallisto (by the cufflinks author), STAR, etc.?