Dear Biobakery Team,
I got an issue using bowtie. I’m analyzing metagnomic data from human gut microbiome (data are Illumina shotgun paired fastq) and I’m employing your pipeline in data preprocessing.
The purpose of my analysis is a precise taxonomic classification of all the samples i have. Briefly, i want to do preprocessing with kneaddata and then feed the cleaned samples in the kaiju  classifier, that only accepts “perfectly matched” paired end files.
The steps involved are trimming (with trimmomatic) and decontamination from human reads. The trimming step is fine, and gives me back paired end files. But when the decontamination step with bowtie2 comes the output is not paired end, and i can not run kaiju on it. Here i attach my settings and a subset of the log-file about bowtie2.
Is there some technical issue about decontaminating that I’m missing? Or something that i do not know about decontamination? Can i rearrange unpaired end outputs in order to get paired ones?