Question: Comparison of RPKM values
0
gravatar for simarsidhu25
2.6 years ago by
simarsidhu250 wrote:

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?

rna-seq • 922 views
ADD COMMENTlink modified 2.6 years ago by Philipp Bayer6.5k • written 2.6 years ago by simarsidhu250
1
gravatar for Philipp Bayer
2.6 years ago by
Philipp Bayer6.5k
Australia/Perth/UWA
Philipp Bayer6.5k wrote:

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/

ADD COMMENTlink written 2.6 years ago by Philipp Bayer6.5k

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

ADD REPLYlink written 2.6 years ago by simarsidhu250
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