How to merge two different flowcell of fastq?

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Richard A. Schäfer

Do you have access on a unix environment? Then simply:

cat file1.fastq file2.fastq > mergedfile.fastq

Lennart F Johansson

I agree with Richard A. Schäfer.

To prevent sample mix-ups I would first demultiplex the fastq files and then merge fastq's per sample.

Fasanella Mariana

thank you! It works!