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, which can be a result of an aligner in Partek Flow or data already aligned before import.

Generating unaligned reads from aligned data gives you the flexibility to remap the reads using either a different aligner, a different set of alignment parameters, or a different genome reference. This is particularly useful in analyzing sequences from xenograft models where the same set of reads can be aligned two different species. It may also 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 reads data node and click Convert alignments to unaligned reads task in the task menu (Figure 1). 

Figure 1. Convert alignments to unaligned reads

A new data node will be generated containing FASTQ files (Figure 2) . Note that the files generated are compressed and the filenames are *.fq.gz. 

Figure 2. Unaligned reads generated from aligned reads

During the conversion, the BAM files are converted to FASTQ files.  The name of the BAM files will be based on the sample names in the Data tab. 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. An example  in Figure 3 shows 18 FQ.GZ files from 9 BAM files.

Figure 3. Task details of unaligned reads generated from aligned paired end samples

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