Code:
bismark -1 Non-overlappling_reads_1.fastq -2 Non–overlappling_reads_2.fastq Merged_overlappling_reads.fastq
I am not quite sure however if merging and making things complicated isn’t exactly doing exactly what the methylation extractor is doing anyway: mapping non-overlapping reads and getting the information from both reads, and only getting the information once from overlapping reads because of the --no_verlap option (isn’t this the same as your ‘merghing’ step?)
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