I recently used jellyfish with some paired-end reads to count k-mers, and I saw another post that mentioned you should concatenate the paired-end reads before inputting into jellyfish.

My question is: is that right? Wouldn't that duplicate the number of k-mers? I used this command:

jellyfish count -C -m 21 -s 1000000000 -t 10 *.fastq -o reads.jf

Which, if I understand correctly, the -C means that it treats both forward and reverse k-mers as valid? Should I redo it, without the -C switch?