I ran Metaphlan3 on human stool samples generated from Illumina HiSeq 2000 platform to generate approximately 8 Gb of 150 bp, paired-end, reads per sample (mean 7.9 gb, st.dev 1.2 gb) with
metaphlan <sample.fastq> --input_type fastq --nproc 16 -o_metaphlan.txt --tmp_dir --bowtie2db --force --add_viruses -t rel_ab_w_read_stats --unknown_estimation
My question is whether I can merge this table with another Metaphlan3 table ran without
unknown_estimation? Can I remove the unknown category then re-scale, and merge the two tables? Related to that, in the case when you don’t estimate the unknown, where does those reads end up? Are they simply removed?