#Question

[JiaZhong28]

hi, I wonder what's the difference when metaPhlan deal with paired-end reads and single reads? I run my paired-end data with wrong command ("metaphlan fastq1 fastq2 -o") ,which end with a re-write bowtie2out to my raw data(a bowtie2out named fastq2 rewrite the raw fastq2), and a result which actually result from only one file in paired end. my question is that, if it's necessary to use only one file in pared-end reads for metaPhlan to qualified the tax abundance instead of two?

[github-actions]

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