Say my goal is to identify SNPs or Differentially expressed transcripts between 3 main groups:
1. High Fat 2. Medium Fat 3. Low Fat
For each group I have 3 biological reps (3 distinct progeny from a specific cross) and 2 technical reps of each biological rep.
High Fat contains 3 biological replicates of a cross between
Parent_1 x Parent_2
Medium Fat contains 3 biological replicates of a cross between
Parent_3 x Parent_4
Low fat contains 3 biological replicates of a cross between
Parent_5 x Parent_6
Each of these biological replicates has 2 technical replicates.
I know that standard protocol suggests concatenating the technical reps and then aligning (and eventually merge biological reps with read groups), but if my objective is to detect SNPs or DE transcripts between the 3 main groups (i.e. the 3 distinct families which represent each group) should I consider concatenating biological and technical reps before aligning?
Possibly a poor question, but would appreciate any feedback.