Hello John, Perhaps you have found this tool already, but "NGS: QC and manipulation -> FASTQ interlacer on paired end reads" can merge the two paired FASTQ files into a single input for Mosaik. Very sorry for the delay in reply, a few questions slipped through in May, Take care, Jen Galaxy team On 5/27/11 8:57 AM, John David Osborne wrote:

Hello, I’m trying to run Mosaik on our galaxy instance on Ilumina paired reads. However when I selected “paired reads” and Ilumina as an input option, I can still only select one of the two fastq files as input. No 2nd file selector appears like with bwa, bowtie, etc...

Can anybody tell me what is going on – is this a known issue?

-John

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