Aligned reads data can be converted to unaligned reads in Partek^® Flow^®.  The The task is available under Post-alignment tools in the task menu when the user selects any aligned Aligned reads data node is selected, which can be a result of an aligner in Partek Flow or data already aligned before import.

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To perform the task, select an aligned Aligned reads data node and click Convert alignments to unaligned reads task in the task menu (Figure 1). 

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During the conversion, the BAM files are converted to FASTQ files and a new Unaligned reads data node will be generated (Figure 2) . 

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The filenames of the FASTQ files will be based on the sample names in the Data tab. The files generated are compressed with the extension *.fq.gz. For samples containing BAM files with paired end reads, two FASTQ files will be generated for each, and the files names will be appended with _1 and _2. An example in Figure 3 shows 18 .fq.gz output files that came from 9 BAM files.

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