EDIT: I have created a new post to address the remaining unanswered part to this question: Connect gene names to GO terms/function for loading in DESeq2
Hi, I want to ask how to go about doing differential expression analysis after getting gene counts with STAR. I would also like to connect the gene names to GO terms before loading them into DESeq2. The counts are from mouse reads mapped to the genome and annotation files from GENCODE.
I seen in another post someone's counts looking like this:
Sox17 9368 81 9287
Mrpl15 4473 30 4443
Lypla1 3122 20 3102
Tcea1 397 6 391
Mine look like this, without gene names:
ENSMUSG00000095475.1 5 0 5
ENSMUSG00000094855.1 0 0 0
ENSMUSG00000095019.1 0 0 0
ENSMUSG00000095041.7 919 16 903
I intend on making graphs similar to this (taken from the paper that performed this study already): http://cancerres.aacrjournals.org/content/canres/78/5/1334/F5.large.jpg.
Not sure what to do. I appreciate the help.
