# Help for metaPhlan3 with paired-end reads
**URL:** https://forum.biobakery.org/t/help-for-metaphlan3-with-paired-end-reads/5176
**Category:** MetaPhlAn
**Created:** [April 21, 2023, 2:03am UTC](https://forum.biobakery.org/t/help-for-metaphlan3-with-paired-end-reads/5176 "2023-04-21T02:03:55Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@jiazhong28](https://forum.biobakery.org/u/jiazhong28)
#### Post date: [April 21, 2023, 2:03am UTC](https://forum.biobakery.org/t/help-for-metaphlan3-with-paired-end-reads/5176/1 "2023-04-21T02:03:55Z")
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?
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### Author:  [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)
#### Post date: [April 21, 2023, 7:52am UTC](https://forum.biobakery.org/t/help-for-metaphlan3-with-paired-end-reads/5176/2 "2023-04-21T07:52:48Z")
Hi @jiazhong28
For running metaphlan with more than 1 FASTq file, you should specify the files separated by comma (wo spaces) e.g. `metaphlan fastq1,fast2 ...`
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### Author:  [@jiazhong28](https://forum.biobakery.org/u/jiazhong28)
#### Post date: [April 21, 2023, 8:09am UTC](https://forum.biobakery.org/t/help-for-metaphlan3-with-paired-end-reads/5176/3 "2023-04-21T08:09:50Z")
thanks for your reply, i’m still wondering that if it necessary for me to simply regared paired-end file as doubled results from just fastq1 only, since that metaphlan do not use paired information for abundabce caculation?
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### Author:  [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)
#### Post date: [April 21, 2023, 1:28pm UTC](https://forum.biobakery.org/t/help-for-metaphlan3-with-paired-end-reads/5176/4 "2023-04-21T13:28:57Z")
Even if MetaPhlAn does not use the paired-end information, markers not mapping to one of the ends could still be mapping to the other read pair when the mapping region is one of the ends of the marker. So I will still recommend using both pairs when executing metaphlan