I used the default parameters for metaphlan3 to analyze trimmed metagenomic reads from a glacial sample. I do not get many hits (wc -l profiled_metagenome.txt == 31) and they are dominated (97%) by cyanobacteria, which I do not think corresponds to the composition of the sample very well. I have seen mentioned in other threads to lower --stat_q and --min_mapq_val for environmental samples. I understand --min_mapq_val , and I think I do not want to lower that much. I do not understand --stat_q. Can anyone explain stat_q to me? Does anyone have any thoughts on minimum values for these parameters for which the results would still be trustworthy?
Or maybe the compositioin of my sample is just not well represented in the marker gene database? I do not think data quality is the problem because assembly and binning went very well.
Finally, can I use my bowtie2 output from the default run as an input when I change parameters? Or do these parameters affect the creation of the bowtie2 output?