The bioBakery help forum

Extraction of mapped reads

Hi,

While using MetaPhlAn3, is it possible to extract the reads (16S rRNA and/or marker gene sequences) used for the taxonomic assignment of the query sequences?
I am using a combination of meta-genomics and culture dependent approach. I wanted to specifically extract the gene sequences related to Lactobacillus plantarum from my metagenome data.

Thank you
Kunal

Hi Kunal,
You can extract the all the marker genes for your species using the extract_markers.py script included with MetaPhlAn by running extract_markers.py -c s__Lactobacillus_plantarum -o lactobacillus_p_markers and then screen the bowtie2out file to determine which markers were mapped to the metagenome.

Hello Francesco,

Thank you very much for your response and the solution.

Best,
Kunal