How to Extract Unaligned Reads From a BAM
BAM files are binary formats of sequencer readers. They store scientific nucleotide data in a compressed format, mixing both aligned and unaligned reads together. They are controlled with the “bam2fastq” tool, a computer command that comes installed with many nucleotide-sequencing programs (you can also get it for free.) To extract the unaligned reads from a BAM file, then, all you need is the Windows command line.
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Instructions
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Type “bam2fastq” into the Start menu search bar to make sure you have the tool (you don’t need to open it.) If you do not, get it for free in Resources.
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Type “cmd.exe” into the Start menu search bar. Click “cmd.exe” when it appears above. This opens the windows command line.
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Type “bam2fastq --unaligned FILELOCATION.bam” (no quotes) into the command window.
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Replace “FILELOCATION” with the location of the BAM file. Use the format C:\Folder1\Folder2\File.bam.”
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Hit "Enter." This will pop up a text window with the unaligned reads from that particular BAM file.
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