Can all R1 and R2 files be combined prior to interleaving?

[reliscu]

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

[GenoMax]

What are these files from? If you need to create a single file per sample then you should do the following. Cat all R1/R2 pieces together and finally interleave.

cat R1_1.fastq R1_2.fastq R1_3.fastq > R1.fastq
cat R2_1.fastq R2_2.fastq R2_3.fastq > R2.fastq

Finally

in1=R1.fastq in2=R2.fastq out=Sample_interleaved_reads.fastq