Tag: StrainPhlAn

Polymorphic rate and single dominant strain – StrainPhlAn

fancyge January 28, 2023, 12:42pm #1 Hi Aitor, I wanted to ask about the .polymorphic file. Is percentage_of_polymorphic_sites the same as the term polymorphic rates? Is this calculated as number of polymorphic sites/ number of all concatenated markers? In strainphlan3, is the polymorphic_sites marked as “-“ in concatenated.aln and folder…

Continue Reading Polymorphic rate and single dominant strain – StrainPhlAn

StrainPhlan clade “s__Akkermansia_muciniphila” not accepted and should provide in SGB format – StrainPhlAn

raminka January 28, 2023, 1:27am #1 I want to run strainphlan4 on my metagenomics data to get the strains of the “s__Akkermansia_muciniphila”. However, following the tutorial for strainohlan4 pipeline, the clades are specified in SGB format. So I cannot pass “s__Akkermansia_muciniphila” as the option of the extract_marker step:extract_markers.py -c s__Akkermansia_muciniphilaor…

Continue Reading StrainPhlan clade “s__Akkermansia_muciniphila” not accepted and should provide in SGB format – StrainPhlAn

Extract_markers.py: input database path format – StrainPhlAn

From the extract_markers.py script docs, it is not clear how the –database path should be formatted. I originally tried using 4.0.3, which is the directory name holding all of the bowtie2 db files, but I received the error: Could not locate a Bowtie index corresponding to basename “4.0”. After looking…

Continue Reading Extract_markers.py: input database path format – StrainPhlAn