kdc10
commented
3 months ago - A lower minimum abundance will be able to include lower abundance species in your results, but are also likely to induce more false positive claims. We set the default based on our experimentation.
- In general, more reads provide more insight. We have not run experiments exploring these values, thus we cannot make any claims here.
- I believe the "minimum reads" you are referring to here is essentially the value for the min-abundance threshold. We do not set this minimum in terms of a count integer, but rather an abundance (proportion of all the reads). Thus if you want a certain minimum read count, you will have to do a quick calculation incorporating the total number of reads in your sample.
Emu has a default minimum abundance. Wanted to know if you have any data to show that to what extent we could lower the minimum abundance score. I have kept it to 10 (to the power of -8). If we lower the minimum abundance score to even lower levels will we be able to get more species in our list ?
Secondly, I wanted to know which is the recommended amount of reads that a stool profile should give in order to get a good idea of the gut microbial spectrum in the sample. Our sample is giving around 30-35K reads from the Nanopore Flongel flow cell.
Lastly wanted to inquire, at what minimum reads does the emu pipeline detect a species ? Is there a way we could set our own threshold of min reads for a species to be detected ?
Please help in the regard