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AnantharamanLab / PropagAtE

Prophage Activity Estimator
GNU General Public License v3.0
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Size Fractionation #9

Open Drob84761 opened 1 year ago

Drob84761 commented 1 year ago

I filtered my samples at .2 microns and then I also sequenced the free floating section. How will this affect my use of your program?

KrisKieft commented 1 year ago

You will probably end up with inaccurate results, or more specifically you'll likely end up finding fewer active viruses than there actually are. If you separate the viruses (most of the under 0.2 micron) from the greater than 0.2 micron fraction then you are separating a lot of the active viruses (their genome copies). You can run propagate on the greater than 0.2 micron and capture some active viruses. You can't really combine the sequencing results from the two fractions because the coverage ratios will not be accurate. You can try running propagate but keep these caveats in mind.

Kris

Drob84761 commented 1 year ago

So even if these samples are cross assembled we still can't compare them accurately?

KrisKieft commented 1 year ago

The discrepancies in coverage will show up when they are sequenced due to differences in read depth and sequence abundances.