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 :
I have 2 questions:
1- Which software can produce these output
2- How can i generate P-value and FDR without replicate? (i mean software)