User: Picasa
Picasa • 560
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Posts by Picasa
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... Hi all,
I have 2 different genomes and I am looking to assess if one assembly is more collapsed than the other one (example: if paralogues are collapsed in one assembly more than the other).
Do you have any idea how can I do this ?
I am also open to papers that have reported this problem too.
...
written 4 months ago by
Picasa • 560
• updated
4 months ago by
colindaven • 2.4k
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Comment:
C: Create de novo repeat library
... Ok I see.
I have also the Repbase database. Do you think it's useful to perform the step
2.3) Blast proteome against RepeatModeler library
on it ? Because they are curated one so it's not necessary no ?
The problem with Repbase is that the header is not formatted properly (ex: `>LINE1-11_SBi# ...
written 4 months ago by
Picasa • 560
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C: Create de novo repeat library
... Thanks for this guide @Juke34,
1) I am a bit confused about what to exclude from the proteome: I made an annotation with maker and should I exclude all genes that are more or less close to TEs ? (like transposase, gag, pol, endonuclease, reverse transcriptase)
2) I would like also to combine the R ...
written 4 months ago by
Picasa • 560
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... Hi @Michael,
Best-scoring ML tree with support values written to: RAxML_bipartitions.[run id] is bootstrap value ? I am interested in it, do you know how to display on figtree ?
...
written 4 months ago by
Picasa • 560
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Comment:
C: ONT fast5 basecalling
... Hi @WouterDeCoster, do you have a guide for basecalling using Guppy ? (I don't have access to the community page) ...
written 4 months ago by
Picasa • 560
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... Thanks,
To infer the phylogeny, do you perform partition analysis with each gene coordinate ? ...
written 4 months ago by
Picasa • 560
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... how many rounds of Arrow would you recommend ? ...
written 4 months ago by
Picasa • 560
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169
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... Thanks ! Do you have any recommendations for the trimming step ? ...
written 5 months ago by
Picasa • 560
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... Hi all,
I have 50 species and 8 genes. My goal is to make a phylogenetic tree but the problem is that I don't have the 8 genes for all species.
Some species have just one gene for example, and also most of the genes are fragmented (so for the same gene, the size is different between species).
Wha ...
written 5 months ago by
Picasa • 560
• updated
5 months ago by
Mensur Dlakic • 7.0k
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... Thanks for your answer.
> Evolutionary constraints/conservation works mainly on those sequences
I am not sure to understand this. Do you mean algorithm used by phylogenetic softwares (such as raxml or phyml or whatever) used model that worked with cds (dna level) and/or amino acid ? ...
written 5 months ago by
Picasa • 560
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