User: Picasa

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Picasa590
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Posts by Picasa

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Comment: C: Transcript or cds for phylogenetic tree ?
... 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 Picasa590
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Transcript or cds for phylogenetic tree ?
... 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. ...
phylogenetic msa written 9 months ago by Picasa590 • updated 9 months ago by lieven.sterck10k
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Comment: C: Workflow for structural variants from long read sequencing data
... Hi, Do you recommend to use corrected pacbio reads (with canu for instance) or raw pacbio reads ? ...
written 9 months ago by Picasa590
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Subset long reads and optimal coverage
... 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. ...
assembly long reads written 10 months ago by Picasa590 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: Structural variation germline vs somatic ?
... Thanks for your paper. Very interesting. ...
written 10 months ago by Picasa590
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Comment: C: Structural variation germline vs somatic ?
... 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 Picasa590
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Structural variation germline vs somatic ?
... 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 ...
somatic structural variation germline written 11 months ago by Picasa590 • updated 10 months ago by metinyazar8810
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Comment: C: How to get Gene ID from NCBI accession for non model species ?
... Thanks for your answer @genomax. I got an issue with the -db option. Which database are u using ? ...
written 11 months ago by Picasa590
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How to get Gene ID from NCBI accession for non model species ?
... 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: ...
ncbi gene id accession written 11 months ago by Picasa590 • updated 11 months ago by GenoMax96k
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Comment: C: RepeatMasker overlap and interpretation
... 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 Picasa590

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