Dear all,
         I am a PhD candidate in Beijing Institute of Genomics, Chinese
Academy of Sciences. Recently I have been worked with data analysis
concerning RNA capture followed by high throughput sequencing. Four
samples, 2 cases and 2 controls, were used for sequencing. My library
preparation protocol is similar to workflow of Exome capture, except for
the material used for capture was cDNA and the capture library was
customized probes synthesized by Agilent.  After mapping, I want to do DEG
analysis utilizing DESeq, and I found the gene number would affect the
results given by DESeq. So my question is whether DESeq compatible with
limited genes (83 candidate genes for my project)? And would you please
give me some suggestions about DEG analysis concerning candidate genes'
RNA-seq? or, for my project, I could just calculate RPKM value for each
gene, and identify DEGs simply by fold change > 2? Thank you!
      Sincerely,

                                   Jianming SHAO

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