I was wondering if someone could recommend the best tool for DEGs analysis? I already used the R package edgeR. Is there any difference between edgeR and DEGseq?
Thanks,
There is no such thing as the best tool for DEG analysis. Every available tool has its advantages and limitations. You should read the vignettes and corresponding papers for these packages and decide by yourself. Seeking for the best package on ResearchGate is really not the way to go.
Depending on how many samples you have, you could always analyse your data with several packages and then compare. I personally used DESeq2 for bacterial RNA-seq analysis and it worked like a charm (as determined by subsequent qPCR validation).
I second Erik Diaz response there is now a rather large volume of studies showing you get more accurate gene expression estimates using a transcript/isoform approach.
An alternative to Kallisto/Sleuth is Salmon/DESeq2. You simply use the txtimport R package ( http://bioconductor.org/packages/tximport/ ) to get gene-levels estimate that works very well with DESeq2 (since takes the bias weights produced byt Salmon into account).
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