I have sequenced metatranscriptomic sample with technical replicate (same extrected mRNA was sequenced twice). Now, whem i assemble them individually with rnaspades, overall i get similiar results between technical duplicate, but there are a few differecnces in expression of a few metabolic transcripts (like in one sample of same set does not show thisparticular transcript of interest while in other it does).
Can i Concatenate the cleaned fastq of technical replicates (as they are from the same RNA source and sequenced using same library) and re-run the assembly. If so, how do i further calculate the raw read abundance? Do i need to take average or total raw read number (which does not make sense as i will be Concatenating the samples)?