Comparison of RPKM values

Question

[simarsidhu25]

I have a question regarding RNA-seq analysis.

I have RPKM values of expressed genes from 3 lines of a plant species. I want to compare these values and to calculate FDR as well as p-value.

which program I can use for this?

Answer 1

[Philipp Bayer]

It sounds like you have no replicates for each of the 3 lines, right? Most software needs replicates to account for biological randomness, and your p-values will be meaningless.

If you really have no replicates, you can use bowtie/cufflinks to get fold changes of expressions and sort those, or run DESeq or edgeR with the appropriate settings, see this discussion: https://support.bioconductor.org/p/40266/

[simarsidhu25]

Thanks for reply Philipp. But I have done denovo assembly by trinity.