Hi, I am wondering how I can get the taxonomic assignments for individual reads using metaphlan2? All I get is a summary table. Thank you.
unfortunately there’s no feature in order to find directly the taxonomy assignment of each read.
In the bowtie2out file, you can extract the ID of the maker to which each read mapped and using the pkl file for identifying the full taxonomy of the marker. Otherwise, the first field of maker IDs contains the NCBI taxonomy ID of the species.
But wouldn’t that only give you the reads that were assigned at species level? By ID of the marker, do you mean the name of the sequence the read mapped to in bowtie? Also what is the best practice for using paired-end reads?
Unfortunately, yes, just the reads that mapped against a marker
MetaPhlAn does not take into consideration the paring information and considers everything as single reads. In case you have paired ends you can provide them to MetaPhlAn by comma separating the filenames
How can I extract the marker ID to identify the taxonomy?
can you share the command here?
If you have downloaded the mpa_v30_CHOCOPhlAn_201901_marker_info.txt file, you can run
cut -f2 <bowtie2out FILE> | grep -Fwf - mpa_v30_CHOCOPhlAn_201901_marker_info.txt
Thank so much.