Hi! I started about a month ago with bioinformatics (so I'm very new to this) and I have some questions for you. Basically, I have 36 paired-end reads fastq files (18 forward and 18 reverse) and I would like to assemble them into contigs. The final goal would be to identify the contigs and phylogenetically reconstruct them. All sequences are RNA.
For QC, I have tried different Trimmomatic parameters on 1 pair of files (1 forward and 1 reverse) and, for now, I have good quality reads. I have verified everything with FastQC. I plan on trying Trinity or Spades for de novo assembly.
My question is: Do I need to do Trimmomatic on all 36 files and THEN try to merge them together to do the assembly? Or do I need to assemble each pair of files individually (so 18 times) and then, in later steps, will merge them together?
Please let me know if what I am asking is not clear enough. Thank you!