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  • Bowtie paired read input format

    Hi there, I have some fastq data that is formatted for use with Trinity, which supports unpaired reads in paired end data (that is, some sequences that are in read1.fastq are not in read2.fastq, and vice versa). Can I use this data with Bowtie? Or does every sequence in read1.fastq have to have a corresponding read in read2.fastq for Bowtie?

  • #2
    I guess best is to try and see on a dummy pair of fastq files what happens when unpaired reads are present. My guess is that bowtie will not like it...

    Good luck!
    Dario

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