Hi all
I m about to sequence 50 samples (shotgun metagenomics) from animal feces (complex metagenomes) using the novaseq 6000: apx 2.5billion reads in each direction. That way I estimate to have apx 50million reads per sample.
I would like however to add 2 positive controls from pure cultures (probably known E.coli strains that we have in the lab). That way i can check if everything is what it should. By adding 2 extra samples I will then have 52 instead of 50 samples in a single lane which will drop the output to apx 48million reads per sample (I can live with that).
My question is: since often some samples end up having more reads than others, do I introduce a bias in this sequencing run and therefore is it probable that my 2 pos controls will have way more reads than the rest of my 50 samples? if they have less reads, i dont care but if they have much more and i end up having a reduced output for the remaining 50 samples that would be a problem...
thanks
P
I m about to sequence 50 samples (shotgun metagenomics) from animal feces (complex metagenomes) using the novaseq 6000: apx 2.5billion reads in each direction. That way I estimate to have apx 50million reads per sample.
I would like however to add 2 positive controls from pure cultures (probably known E.coli strains that we have in the lab). That way i can check if everything is what it should. By adding 2 extra samples I will then have 52 instead of 50 samples in a single lane which will drop the output to apx 48million reads per sample (I can live with that).
My question is: since often some samples end up having more reads than others, do I introduce a bias in this sequencing run and therefore is it probable that my 2 pos controls will have way more reads than the rest of my 50 samples? if they have less reads, i dont care but if they have much more and i end up having a reduced output for the remaining 50 samples that would be a problem...
thanks
P
Comment