I have paired end reads in 2 separate fastq files. I want to take a subset of these reads for a bowtie run to get insert size. I am familiar with how to break up an individual file into 1 million reads (i.e. here: https://www.biostars.org/p/66864/)
My Question: Do I need to ensure my reads are in the same order in each file before I do this? If so, how do I do this?