User: dago
dago • 2.1k
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Posts by dago
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... I am not familiar with the program you are using. But if the result of the analysis are contigs, I guess as a product of a whole genome alignment, I would say that in 99.9% of the case you will have multiple genes on them. Therefore you would need to do 2 things: gene calling and annotation(if neede ...
written 8 days ago by
dago • 2.1k
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Comment:
C: Bacterial de novo genome assembly
... Look these:
https://www.biostars.org/p/120386/
And also a list of tools available is [here][1]. You can check the one that work in windows amongst them.
[1]: https://omictools.com/genome-assembly-category ...
written 20 days ago by
dago • 2.1k
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Comment:
C: Bacterial de novo genome assembly
... check assembly quality with [QUAST][1]
[1]: http://bioinf.spbau.ru/quast ...
written 24 days ago by
dago • 2.1k
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Comment:
C: De novo genome assembly
... what did you try? There are plenty of tutorials out there. What organism do you have? Bacteria? ...
written 25 days ago by
dago • 2.1k
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... Well, my input data are indeed portion of genomes, and I want to find maximal matches amongst them. So for me it sounds quite good. ...
written 10 weeks ago by
dago • 2.1k
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... Thanks for the answer. Why do you think so? ...
written 10 weeks ago by
dago • 2.1k
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... I have a multi fasta containing 100s of gene clusters.
I would like to align them and calculate a % identity.
I tried to use mummer, using the same multi fasta as both query and reference.
At first I thought that it worked really well, but then I saw something odd.
There are two clusters in the mul ...
written 10 weeks ago by
dago • 2.1k
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... A new year just finished and many new exciting discoveries/programs/methods have been published.
In consistency with previous Discussions
https://www.biostars.org/p/128889/
https://www.biostars.org/p/15417/
https://www.biostars.org/p/4858/
https://www.biostars.org/p/171860/
What do you think ...
written 4 months ago by
dago • 2.1k
4
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279
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... The answer to your question is here:
http://computing.bio.cam.ac.uk/local/doc/iprscan-faqs.html
> InterProScan gives me a report file containing some errors from FingerPRINTScan that are weird like : ERROR: Calculation has exceeded maximum allowed complexity Fingerprint PRICHEXTENSN matches thi ...
written 5 months ago by
dago • 2.1k
0
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... I think it really depends on your specific questions. There could be really different approach to follow. For example, if you are interested in only specific genes then a binning would be not the ideal thing to do especially if you have complex samples as sediments or soil.
You can start here:
[Int ...
written 5 months ago by
dago • 2.1k
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