Concatenate F read files & concatenate R read files in attempts for improved transcriptome?

Question

[jammydodger123456]

I have multiple read files across 7 stages of the life cycle of Fasciola hepatica (from the same study). There are replicates for most stages. My question is this; could I concatenate all of the forward reads into 1 file, concatenate all of the reverse reads into 1 file, then undertake a de novo transcriptome assembly? If these is feasible and doesn't 'break' any bioinformatics rules, how likely is this to be an improvement on a transcriptome predicted from a genome? Each rep has approx. 40 million reads if that helps.

Thanks Duncan

[st.ph.n]

I have not used cufflinks for transcriptome assembly, but i have done exactly as you describe, post QC, with Trinity. I also use the in silico read normalization. You can specify replicates downstream after aligning each replicates files (that you concatenated) to the assembly.