I want to assemble a transcriptome using Trinity of a plant lacking of reference genome for running a RNA-Seq experiment afterwards
I have control plants and plants infected with a fungus for 2, 7 and 15 days. And for all these 4 conditions, I have plenty of Illumina paired reads of nice and good quality per separate.
In the way of getting the transcriptome, I have two possibilities - the opportunity of assembling control and infected plants for separate obtaining a total of 4 transcriptomes. - Or I can concatenate and join all of the reads in a common file and get a common transcriptome
These two possibilities are full of subtle considerations, and I just want to learn from your experiences.