My questions is whether it's okay to to combine multiple R1 and R2 fastq files (i.e. resulting in two files: R1.fastq and R2.fastq), and then use those as input for interleaving to produce a single fastq, e.g.:
in1=R1.fastq in2=R2.fastq out = reads.fastq
The alternative would be to keep all files seperate e.g.
in1=R1_1.fastq in2=R2_1.fastq out = 1.fastq
in1=R1_2.fastq in2=R2_2.fastq out = 2.fastq
...etc.
Thanks in advance
in1=R1.fastq in2=R2.fastq out = reads.fastq
The alternative would be to keep all files seperate e.g.
in1=R1_1.fastq in2=R2_1.fastq out = 1.fastq
in1=R1_2.fastq in2=R2_2.fastq out = 2.fastq
...etc.
Thanks in advance
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