We have a time course infection experiment with 12 samples (2 technical replicates and 2 biological replicates per sample). The samples were sequenced on a HiSeq over 2 lanes, 1 x 50 bp reads.
- 24hr_infection1_ lane4
I aligned the samples using Tophat and then converted the .bam files to .sam files and created a counts file using HTSeq for each sample. My questions now are:
- Should the technical replicates be collapsed (add gene counts for technical replicates)?
- How should the design matrix be setup in edgeR?