Extraction of mapped reads

Microbial community profiling MetaPhlAn
1

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

2

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.

3

Hello Francesco,

Thank you very much for your response and the solution.

Best,
Kunal