I have in my hands the file 'merged_abundance_table.txt' and I want to create a heatmap of relative abundance for Genus. How should I rearrange the comand below?
HI Kevin, thanks for the reply. But I had already solved the question. Knowing that it had multiple '.fna', I was able to resolve the issue with the following command sequence:
linux@ubuntu:~$ for f in *.fna; do metaphlan2.py $f --input_type fasta --nproc 4 --tax_lev g > ${f%.fasta.gz}_profile.txt; done
Can you show the first few lines of merged_abundance_table.txt ? ..also, an example of the format you want to produce would help a great deal.
Thanks! Kevin