Comments (9)
Hi @Liqueurdefehling ,
Though this might sound confusing in first place, it is actually the expected behavior. Platon was designed to classify draft contigs and thus extract plasmid-borne contigs. In order to do so, one can adjust sensitivity/specificity values by running Platon in either sensitivity
, accuracy
or specificity
mode via the --mode
parameter.
In addition and besides the above described normal operation, one can also use Platon in order to characterize (NOT classify) all plasmids via --characterize
.
In that context, the above behavior is expected since in characterization mode, Platon executes the full characterization pipeline which is why all contigs are handled as plasmid-borne. I agree that in this case the output might be misleading and this might deserve a little bit of improvement.
from platon.
Thank you for explanation, now makes sense. I had similar results using the --characterize
option. All the contigs were written into the <prefix>.plasmid.fasta
file while the <prefix>.chromosome.fasta
file was empty. Can this be chaged so the plasmids that had hits will be automatically written into a file for further use?
Great tool anyways , thanks a lot!
G
from platon.
I have tried to comapre the two outputs with (bottom, secon cat) and without (top, first cat) the --characterize
option and I am not sure how to interpret the result. Wht the 2 contigs NODE_5 and NODE_11
that were included in the <prefix>.plasmid.fasta
then are not marked as having any plasmid hits, even when using the --characterize
option. Thanks a lot. G
.
from platon.
Hi @Gian77 ,
the --characterize
option simply conducts all characterization tasks without filtering for or predicting any plasmid/chromosome inference. It's just a convenience option to characterize all contigs.
If you'd like to predict plasmid-borne contigs, then you should use Platon in the default mode w/o --characterize
. In your example NODE_5
and NODE_11
are predicted to be plasmid-borne.
from platon.
Hey @oschwengers,
thanks for the explanation, very useful. I am still confused, though, about what the # Plasmid Hits
field means in the --characterize
mode of platon. I have several contigs that have 1 in the characterize mode in that field, should't they match with what predicted in the default mode?
Thanks much!
Gian
from platon.
Hi @Gian77 ,
wel, it depends. Sure, a small contig can have a BLAST+ hit against a reference plasmid. But this might also be a small part of a mobile element or a fragment thereof, for example an IS, transposon or even just a transposase. To filter out these maybe false-positives, Platon screens for contigs with a sufficiently-high RDS. Only after this initial screening step, remaining contigs are characterized. By this, we can significantly speed up the entire process.
from platon.
Hello @oschwengers ,
Thanks for the explanation. So this means that the characterization may be not 100% correct due to the reasons you mention above, while the default mode it is correct since is performed after the screening for possible false positives. In the end I shoudl trust the default mode results, correct?
Thanks a lot,
Gian
from platon.
Well, not exactly. The characterization is correct in terms of the descriptions. This step does not classify by any means, it merely provides all information on all contigs.
For an actual classification (chromosome/plasmid), you should use Platon in the default (accuracy
) mode.
from platon.
ok @oschwengers, will look into the manual. I think I did not specified accuracy
mode when I run it. Thanks a lot,
Gian
from platon.
Related Issues (20)
- Running multiple samples HOT 2
- Interpretation of results HOT 1
- Platon is Time-Intensive HOT 4
- Blast contig results HOT 7
- Permission denied: 'prodigal' HOT 1
- The number of contigs in plasmid.fasta is not the same as the number of contigs in .tsv HOT 3
- Differences between .log and plasmid.fasta file HOT 3
- --meta missing HOT 2
- RDS is always 0.0 HOT 7
- Platon report Mobilization and Conjugation HOT 2
- IndexError: list index out of range error HOT 1
- genome fasta file UNRECOGNIZED HOT 5
- Where can we find version of the RefSeq plasmid database used? HOT 1
- Strange output - is it normal? HOT 2
- Any plans for enabling user to use custom database like COMPASS HOT 1
- Option to see the 'hits' in the results HOT 1
- execution problem HOT 3
- diamond version HOT 2
- Error: No module named 'platon.platon' As #21
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from platon.