Best Tools for Counting Reads before DE Analysis

Question

[oma219]

Hello,

I'm planning on using DESeq2 for DE Analysis and I was wondering what program would be the best to produce the gene counts if I had previously used STAR for Alignment? Also, what other programs could I use for analysis that use the same gene count file because I hoping to compare my results between program? Any help would be appreciated! Thanks.

Omar

[Rohit]

As Wouter mentioned your previous question already has implementable options outlined. You need to go through some literature and tutorials (this, this and this review).

[WouterDeCoster]

Your previous thread When is HTSeq Count Script used? contains already quite some information on that.