Aligned reads data can be converted to unaligned reads in Partek^® Flow^®.  The in Partek Flow. The task is available under Post-alignment tools in the task menu when the user selects any aligned Aligned reads data node (Figure 1).  It is selected, which can be from a result of an aligner in Partek Flow or data already aligned before importing into a projectimport.

Generating unaligned reads from aligned data gives you the flexibility to realign remap the reads using either a different aligner, a different set of alignment parameters, or a different genome reference. This is particularly useful in sequencing samples analyzing sequences from xenograft models where the same set of reads are can be aligned to two different species. It is may also helpful be useful if the original unaligned FASTQ files are not as easily accessible to the user as the aligned BAM files.

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 containing FASTQ files (Figure 2) . Note that the files generated are compressed and the filenames are *.fastq.gz. 

During the conversion, the BAM files are converted to FASTQ files.  If the BAM file contains 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 BAM, and the files names will contain be appended with _1 and _2. In An example in Figure 3 , the example shows 18 fastq .fq.gz output files that came from 9 BAM files.bam files