Files from kneaddata output to use in metaphlan

[JenS]

Hello,
I was wondering if someone could confirm the two paired end files to be entered into metaphlan from kneaddata output. I am pasting the 12 files output from kneaddata after entering 2 paired end files.

Is the correct files to be used in metaphlan: AAA02109_S17_R1_001_kneaddata_paired_1.fastq and AAA02109_S17_R1_001_kneaddata_paired_2.fastq?

Below are all of the paired files that are output from kneaddata are:
AAA02109_S17_R1_001_kneaddata_paired_1.fastq
AAA02109_S17_R1_001_kneaddata_paired_2.fastq
AAA02109_S17_R1_001_kneaddata.trimmed.1.fastq
AAA02109_S17_R1_001_kneaddata.trimmed.2.fastq
AAA02109_S17_R1_001_kneaddata.trimmed.single.1.fastq
AAA02109_S17_R1_001_kneaddata.trimmed.single.2.fastq

AAA02109_S17_R1_001_kneaddata_Homo_sapiens_bowtie2_paired_contam_1.fastq
AAA02109_S17_R1_001_kneaddata_Homo_sapiens_bowtie2_paired_contam_2.fastq
AAA02109_S17_R1_001_kneaddata_Homo_sapiens_bowtie2_unmatched_1_contam.fastq
AAA02109_S17_R1_001_kneaddata_Homo_sapiens_bowtie2_unmatched_2_contam.fastq

AAA02109_S17_R1_001_kneaddata_unmatched_1.fastq
AAA02109_S17_R1_001_kneaddata_unmatched_2.fastq

Thanks!

[shengxinf]

I think you are right, and you can put “AAA02109_S17_R1_001_kneaddata_paired_1.fastq” and “AAA02109_S17_R1_001_kneaddata_paired_2.fastq” into metaphlan3 to analysis. In kneaddata github,we can see that:

so I think they are the files that you can use and analysis.(sorry ,my English is poor…)I hope it helps!