User: Picasa
Picasa • 590
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0
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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 9 months ago by
Picasa • 590
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... Hi,
I would like to make a single phylogenetic tree after a multiple alignment of sequences of differents species.
For the sequences, should I use the whole transcript or only de CDS part ? or it doesn't matter.
Thanks for your help. ...
written 9 months ago by
Picasa • 590
• updated
9 months ago by
lieven.sterck ♦ 10k
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... Hi,
Do you recommend to use corrected pacbio reads (with canu for instance) or raw pacbio reads ? ...
written 9 months ago by
Picasa • 590
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... Hi,
I was wondering what is the optimal coverage for long reads assembly if I want to subset my reads (by size, quality or whatever).
Is there any benchmarks that have been done ?
Thanks. ...
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229
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... Thanks for your paper. Very interesting. ...
written 10 months ago by
Picasa • 590
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... I am working with a non model species and don't have a normal-tumor samples.
But rather 2 haplotypes, and I am expecting one haplotype (let's call it hap B) to have a specifc inversion. Do you think I can "transpose" it like a normal-tumor samples so that would be hap A for normal and hap B for tu ...
written 10 months ago by
Picasa • 590
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5 follow
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... Hello,
I have tried multiple tools to call structural variants like Manta, Delly etc. They all have a germline or somatic mode.
I couldn't find this information anywhere but anybody know how these structural variant callers determine how a variant is a germline or somatic one ? What are the crite ...
written 11 months ago by
Picasa • 590
• updated
10 months ago by
metinyazar88 • 10
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... Thanks for your answer @genomax.
I got an issue with the -db option. Which database are u using ? ...
written 11 months ago by
Picasa • 590
2
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1
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202
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1
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... Hi all,
I have a non model species so R packages where you specify your genome/annotation don't work and I also tried `https://david.ncifcrf.gov/conversion.jsp` but got no result.
I have an accession (ex: `XP_025269744.1`) and want to retrieve the GeneID (ex: `112639560`).
Example with this link: ...
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... Thanks for your answer, it's more clear.
However, sorry but I am not familiar with this output but how did you calculate 1900 bp ?
I have looked at the sequences `rnd-1_family-52#DNA/Maverick` and `rnd-1_family-50#Unknown` generated by `RepeatModeler` and their size are `6975 bp` and `1116 bp` re ...
written 11 months ago by
Picasa • 590
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