Hello guys,
I sequenced RNA from whole individuals from 4 different experimental conditions (non-model isopod species). The thing is that I used different library prep protocols:
- Condition 1 and condition 2: samples were made with library prep kit X (stranded, reverse–forward)
- Condition 3 and condition 4: samples were made with library prep kit Y (stranded, forward – reverse)
My idea is to assemble De NOVO transcriptome from all these samples.
Question 1: Is it OK to do that since in Trinity you have to choose strandedness and I have 2 different kinds of lib protocols. Can I for example reverse all the reads from samples coming from the one library prep type and then use reads from all samples together for the de novo assembly?
Question 2: if I can do the assembly like described, can I do the differential gene expression analysis? My final goal is to map each sample to this Denovo transcriptome and do DGE analysis but my comparison groups will still be from the samples coming from the SAME library production type - meaning I will compare condition 1 VS 2 on one hand, AND condition 3 VS condition 4 on the other (so there will be no comparisons between samples coming form different library types).
