I have read your paper on bioBakery3 and I am using metephlan3. Thanks for making it available and it is a really good tool. I want to do alpha diversity and DESeq2 on the taxa and need to use absolute reads counts. So I used the code as with additional flag of “-t rel_ab_w_read_stats” :
metaphlan r1.fastq.gz, r2.fastq.gz -t rel_ab_w_read_stats -o s1.tsv --input_type fastq —bowtie2out s1.bowtie2.bz2 --nproc 4
In the output file, there is
My questions are:
- Are “estimated_number_of_reads_from_the_clade” the absolute reads counts for specific taxa?
- There is also “coverage” column? What does it really mean? Should I filter the output table with this coverage number to get a good taxa table? If so, which number would be good to use?