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You can optionally directly specify the output fastq filenames using:
You can optionally directly specify the output fastq filenames using:
* --firstOut firstReadInAPair.fastq (also used for the interleaved filename with [[#Generate 1 Paired-End Output File (--merge)|<code>--merge</code>]].
* --firstOut firstReadInAPair.fastq (also used for the interleaved filename with [[#Generate 1 Paired-End Output File (--merge)|<code>--merge</code>]])
* --secondOut secondReadInAPair.fastq
* --secondOut secondReadInAPair.fastq
* --unpairedOut unpairedReads.fastq
* --unpairedOut unpairedReads.fastq
