Hello,
I was wondering if anyone had advice on the best program to use for DE Analysis after using STAR for alignment? I'm not sure whether to use CuffLinks or DESeq. Also, do both of them accept .bam files that are produced by STAR. Thanks.
Omar
Actually I would give a try to Sleuth, the DE tool based on pseudo-alignments. Is by far the most user friendly, accurate and easy to use. It has other advantages, take a look: http://pachterlab.github.io/sleuth/
You will have to run kallisto or salmon to get the quantification (it does not rely on traditional alignments.). These programs are super fast and can be even run on a laptop in minutes.
It's worth noting that Sleuth does have it's drawbacks if you have a more complex experimental design than A vs B, at least it did when I last used it, and that's not to say that I know of any other solid alternatives. Additionally, you can use Salmon to quantify (similar concept to Kallisto), and put it through Wasabi to make it ready for Sleuth
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version 2.3.6
Most people here would advice to use DESeq2, or similar tools such as limma trend/voom or edgeR.
You'll have to get raw read counts first from your bam files, I prefer using featureCounts for this.
Is Cufflinks also a possible option for DE analysis or is it used more in other situations? Thanks!
Cufflinks is no longer advised software for RNA-seq analysis, an updated pipeline is described here.
Thanks! So would you agree that DESeq2 is one of the better programs to use for DE Analysis? I just finished the alignment with STAR so I was trying to decide which programs would be best.
DESeq2 is indeed a very good tool to do gene expression analysis. You can go for it. The R vignette is well done and you can find a lot of tutorial by googling it.