Hello there, I am facing problem in interpreting Rockhopper output. I have bacterial RNAseq data which is single end and 50 bp read length. Reference database is available. There are duplicates for both the samples. I ran Rockhopper using following parameters checked "Reverse complement reads" and "Test for differential expression", but did not get any information regarding fold change. Also I got only Qvalues. I don't know how to find upregulated and downregulated genes from this output. The columns which I got in transcripts.txt are: Transcription_Start, Translation_Start, Translation_Stop, Transcription_Stop, Strand, Name, Synonym, Product, Expression_Control, Expression_Treated, qValue_Control vs Treated.
Any help would be much appreciated!! Thanks and regards!