Hello, I am trying to do some differential expression count on RNA Seq data using Galaxy. I did an alignment to reference genome and uploaded the files on the galaxy and did HTseq count and then Deseq2. My experiment set up is such that I have 6 duplicate samples for control and 6 duplicate for experimental group collected at 6-time points across the 24hr cycle(2hr, 6hr,10hr,14hr,18hr,22hr). So while using Galaxy I chose Factor level 1 as control and selected all the control file and did same for the experimental group. I have to further analyze these data to look out for the genes those were having circadian rhythms upon treatment. So I checked for normalized read counts generated by Deseq2. Here lies the problem, The results show normalized values for both groups labeled as 1,2,3,4....12 (Control 1, control2......control12, experimental 1, experimental 2.......experimental 12). I need precise values for every time point in order to see which all genes are expressed in a circadian manner. Is there any way to do this?
Thanks for your help.
