Paired End Run output explanation

Infrastructure and utilities KneadData
1

Hi everyone,

I get some output files after running Kneaddata, including kneaddata_paired_1.fastq and kneaddata_paired_2.fastq. I thought these two output files are aligned to the reference database I chose.

But in the GitHub official website, it’s saying " kneaddata_paired_1.fastq : Reads from the first mate in situation (1) identified as NOT belonging to any of the reference databases." that shows in the below screenshot. (For my understanding, situation (1) means “1. Both reads in the pair pass.”)

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Could someone explain this to me? Plus, can I use these two files for downstream analysis?

Thanks!

2

For my understanding so far, the bowtie2 reference databases contain contaminant sequences, that we want to remove if they exist in our samples. Therefore, the sequences remaining in paired1 and paired2 output files are identified not only as paired (“situation (1)”), but also as not belonging to any reference databases we have chosen. Otherwise, they will go to “contam.fastq” files. We can use paired1 and paired2 fastq files for downstream paired-end analysis.

Reference: https://learn.gencore.bio.nyu.edu/metgenomics/quality-control/