I have a set of FASTQ files that I want to align to the reference genome. The sequencing for each sample has been done on 2 different runs (flow cells) and 2 different lanes so for each sample I have 4 files. I am not sure when I should merge my files, before or after alignment? I read previous posts that suggest to merge the samples after alignment, but I am not sure what is the best in my case. Could I merge the samples using samtools? Do I just simply cat one at the end of the other?
An example for sample1 is shown below (FC = flow cell, L = Lane)
Thanks a lot in advance!