What does the maker in clade flag do?

[Feargal Ryan]

Hi, 

I've been trying to find an answer to this but I'm not 100% on what it actually does. It states the percentage of marker genes that need to be detected in order for a sample to be included? 

I ask because I ran into an issue profiling B. longum and it would only include my reference genome if this was dropped to 0.5. 

What are some of the consequences of dropping this lower? I was interested in including an outgroup reference strain for comparison so i guess this parameter would need to be dropped quite low. 

Thanks

[Aitor Blanco-Miguez]

Hi Feargal,

The marker_in_clade parameter establish a threshold for filtering samples (and reference genomes) with not enough markers for the clade you are interested on.

This means that, in each sample (or ref. genome), if the clade you are interested on presents a percentage of reconstructed markers less than the marker_in_clade parameter (the percentage of markers is calculated based on the number of markers available in the metaphlan2 database for the clade), the sample is not taken into consideration in the analysis.
If you lower this parameter, samples with less reconstructed markers for the clade will appear on your analysis. Then, if you should drop the parameter until 0.5 to include your ref. genome in the analysis, that means that your genome only present 50% of the B. longum markers of the metaphlan2 database you are using.

I hope this helps.

Best,

Aitor