I have paired end reads from Illumina NextSeq. I've removed adapters/primers, quality trimmed, and interlaced the forward and reverse reads. I now have a single fasta (not fastq) file with the following structure:
>NS500647:208:HYKFFBGX2:1:11101:9580:1154 1:N:0:GATCAG GTGGTCAGCAGACGTTTAGCTTCGTCAACCAGGTCAGCTTCGTACAGGGATTTACAGATTTCAGGG >NS500647:208:HYKFFBGX2:1:11101:9580:1154 2:N:0:GATCAG ACTGGNNNTTCTGGAAAANNNNNGNNTCANC >NS500647:208:HYKFFBGX2:1:11101:24675:1156 1:N:0:GATCAG AGCCGATATTCACTACCTGCTCGCCTTTAACGTTCGCAATGTCTTTTAGTTGCGGCACCGCATTAACCAGA >NS500647:208:HYKFFBGX2:1:11101:24675:1156 2:N:0:GATCAG CGCACNNNATATGGGTTTTANTGGNGCAGCAT
Is it possible to merge the R1 and R2 reads into a single fragment? Or is that not how the paired end reads work?