In a work to identify the DEGs in Rice (control Vs treated), I used Tophat->Cufflinks->Cuffdiff pipeline. However, at the final stage, I get multiple FPKM values per gene. I really dont know how to deal with those multiple FPKM. Anyone who has solved the issue is kindly requested to share the solution. Thank you..
Note: Following a forum I tried to use ' --no-novel-junctions' in Tophat, but it didnt work.
I would suggest to work with HTSeq count data and DESeq2 pipeline for DEG analysis, once you have mapped your reads with tophat.
for DEGs, you have more trustworthy results through this pipeline than with Cuffdiff.
there is always FPKM variability, mostly for the genes which are smaller in size., you can normalize them with sva package from bioconductor.
or may be because of differential splicing patterns , these problems are arising in your case, you can check it by DEXSeq package.
HTH
Thanks for the suggestion Manvendra Singh. As you suggested, I will have to move to DESeq2 pipeline.
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