I'm new to doing bioinformatics so bear with me.
My experimental design is as follows:
- 4 timepoints (3d, 7d, 14d, 56d)
- 2 conditions, each with time matched controls
- For every condition, there are 5 replicates per time point, 3 replicates for each time-matched control
That is, condition 1 at 3d has n = 5, and control of condition 1 at 3d has n = 3 etc...
The core facility provided the complete cufflinks output and provided a merged.gtf file that was made from cuffmerge.
How do I:
- Find DE genes between every time point of each condition and its time-matched control? Do I do individual EdgeR at every time point or is deseq or cuffdiff preferred?
- Find DE genes between the conditions (should I just filter for the genes DE to controls as found in #1?)
- Find the biological pathways (GO/KEGG) that are distinct between the two conditions?
- How do I then visualize these distinct networks (e.g. put them into figures), cytoscape?
Package names would help a lot, I have some proficiency in R and Java.
Thanks so much in advance!