I'm de novo assembling a transcriptome. I have RNA-seq data of treatment and control group with two time points. There are three replicates for each group. When doing the assembly, shall I pool all reads (from both control and treatment groups) to assemble or just use each replicate to do the assembly? Is it ok to pool them together and if assembling for each replicate what I shall do to make it comparable between different groups and differenet timepoints? Thank you.