I have two FASTQ data sets/files (read.R1.fastq and read.R2.fastq) generated from paired-end read sequencing. One file (read.R1.fastq) contains 18 nucleotide long linker/tag. How can I extract the reads containing the linker (allowing 3/4 mutations inside it) from read.R1.fastq and its corresponding reads from read.R2.fastq and save the extracted reads into two separate files? Is it possible to prepare a single file after extraction which will contain the full-length sequence of reads and their information (such as ID, quality score, etc.)?
Thanks in advance.