integrated_prophages_detector.py troubleshooting and interpretation

[EleftheriaCha]

Hello,
I am interested in using the post-processing integrated_prophages_detector.py script in order to clarify through an NGS metagenomic dataset what is "phage", what is "bacterium" and what is a "prophage". Upon running the script we get an output just as in your description. However, in particular samples it seems that the chimeric reads count is larger than the identified bacterial count. Is that normal?

[meenachakra]

Thanks! Tagging @yipinto who may be able to provide more insight.

[yipinto]

Hello,
If I understand it correctly, yes it makes sense. But can you please send an example? Also can you explain a bit your goal- Phanta just offers evidence "suggested" prophages. Yishay

[EleftheriaCha]

Hello @yipinto the way I understanding is that normally there must be overlapping reads of which from the total viral and total bacteria make up the chimeric pairs. So it is confusing when chimeric pairs have a higher count over the total bacterial. My goal particularly is to try to distiguish between the counts of a particular phage-host pair, but I understand that phanta gives an overview and not particular info on specific pairs. is that correct?

[yipinto]

So for each pair of virus-bacteria you get the number of reads that supports it. It is a specific info on specific pairs.
The thing I'm not sure I understand is- what do you mean by "higher count over the total bacterial".
Can you attach an example?

[EleftheriaCha]

hey @yipinto for example:

So, here I see a total overall count. I do not see info on particular pairs. And, at some point you see bacteria identified 550 where chimeric pairs are 4000+. How do you interpret this and how do you extract info on particular bacteria–phage pairs?

[yipinto]

The first two columns are the taxonomic IDs of the phage and bacteria respectively. The third column is the number of reads supporting it.

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