Best Tools for Counting Reads before DE Analysis
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
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Your previous thread When is HTSeq Count Script used? contains already quite some information on that.
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).