I have 2 RNAseq samples before and after treatment to give a total of 4 files of FastQ
When I look for DEG using Cuffdiff I get different answers compared to using DESEQ2.
The DEG set are mostly different with min overlap.
Raw counts from HTSeq are different from FPKM.
So which set of results do you use, the cuffdiff or the DESEQ2 results ???
When I look for DEG using Cuffdiff I get different answers compared to using DESEQ2.
The DEG set are mostly different with min overlap.
Raw counts from HTSeq are different from FPKM.
So which set of results do you use, the cuffdiff or the DESEQ2 results ???
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