I have a set of meta-RNA-Seq fastq data from bacterial communities. They should be depleted for rRNA, but I want to test the performance of the depletion step.
I have analyzed two paired-end data (#1769, #1770) from the meta-RNA-Seq dataset and compared it to RNA-Seq data (from poly-A sequencing, #516) and to 16S Amplicon-Seq data (#324).
The amount of rRNA reads in the meta-RNA-seq data are ca. 20-30% (analyzed by RiboDetector or SortMeRNA)
However, I was not able to assign rRNA reads from one of the two meta-RNA-Seq data (#1769) to any bacterial taxa.
However, this is also true for the RNA-Seq data (ok, only 3% is rRNA), but alos for the 16S amplicon-seq data (almost exclusively rRNA reads).
Is there an explanation for this. I was searching for optional parameters related to taxonomic classification, but could not find anlything.
The command was: metaphlan (FILENAME).fastq.gz --input_type fastq -o profiled_(FILENAME).txt --nproc 24 --bowtie2db PATH_TO_BT2-INDEX/metaphlan_bt2/ --unknown_estimation