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  • Bowtie2 output fastq of paired reads where at least one in the pair aligns

    Bowtie2 has the option on paired reads to spit out fastq files of things that fail to align concordantly (--un-conc <path>), and it has the option to spit out fastq files of things than align concordantly (--al-conc <path>).

    What I want though, is it to spit out paired reads (a 1 and 2 fastq file) for those paired reads where one of the pair aligns. --I will then be aligning those output paired fastq files to a difference reference.

    Is there a way to do this, or maybe to run the alignment and use samtools view on the bam file to extract reads that hit one of the pair and turn that back into a fastq or align what's in there to a different reference?

    Thanks

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