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

Generating unaligned reads from aligned data gives you the flexibility to realign using either a different aligner or a different genome. This is particularly useful in sequencing samples from xenograft models where the same set of reads are aligned to different species. It is also helpful 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 reads data node and click Convert alignments to unaligned reads task in the task menu (Figure 1). 

A new 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 paired end reads, two FASTQ files will be generated for each BAM, and the files names will contain _1 and _2. In Figure 3, the example shows 18 fastq.gz files from 9 .bam files