Hi friends
I have project on Rice RNA-Seq, in this project i have only 1 replicate for each of 3 conditions.(N,M,S) I should to say, Number of mapped reads (using tophat2) for conditions are:
N= 14,640,080
M= 14,764,894
S= 14,935,162
And you can see "S" has more mapped reads( in contrast with other ~17000 and ~29000).
I analyzed with cuffdiff (with blind mode) which generates:
N_vs_M=30
N_vs_S=350
M_vs_S=319
I know N_vs_M=30
has a problem in gene count and not fine.
I can not find out the problem , i also used DESeq,DESeq2 and edgeR but they could not show any significant DE genes.
I literature review and found same project where done by BGI company, i could not gain any information about the analysis process. They produced these columns:
geneID
geneLength
A-Expression
B-Expression
A-RPKM
B-RPKM
log2 Ratio(B/A)
Up-Down-Regulation(B/A)
P-value
FDR
I have 2 questions:
- Which software can produce these output
- How can I generate P-value and FDR without replicate? (I mean software)
Thanks
Hello pcsam.2008!
It appears that your post has been cross-posted to another site: SEQanswers
This is typically not recommended as it runs the risk of annoying people in both communities.
Do you have another idea about this paper "Transcriptomic Analysis of Rice (Oryza sativa) Developing Embryos Using the RNA-Seq Technique" , they have only 1 sample per condition and also said:
What do you think about this issue? - I mean 1 sample and FDR 0.001 and FC=2
How is it possible?
Thanks
This should probably be its own post.
Having said that, that paper should have been rejected.