User: Picasa

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Picasa590
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Posts by Picasa

<prev • 305 results • page 1 of 31 • next >
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Comment: C: Using HiCanu assembler on PacBio Hifi reads
... what kind of settings ? ...
written 4 weeks ago by Picasa590
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Assessing collapsed assembly ?
... 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. ...
assembly collapsing paralogue written 6 months ago by Picasa590 • updated 6 months ago by colindaven2.5k
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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 6 months ago by Picasa590
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Comment: 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 7 months ago by Picasa590
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Comment: C: RAxML outputs: which one I have to take ?
... 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 7 months ago by Picasa590
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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 7 months ago by Picasa590
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Comment: C: Best way for phylogenetic tree with missing data
... Thanks, To infer the phylogeny, do you perform partition analysis with each gene coordinate ? ...
written 7 months ago by Picasa590
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... how many rounds of Arrow would you recommend ? ...
written 7 months ago by Picasa590
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Comment: C: Best way for phylogenetic tree with missing data
... Thanks ! Do you have any recommendations for the trimming step ? ...
written 7 months ago by Picasa590
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Best way for phylogenetic tree with missing data
... 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 ...
phylogenetic tree written 7 months ago by Picasa590 • updated 7 months ago by Mensur Dlakic8.1k

Latest awards to Picasa

Great Question 4 weeks ago, created a question with more than 5,000 views. For Coverage per contig from a BAM file
Student 10 weeks ago, asked a question with at least 3 up-votes. For Best strategy for de novo assembly with illumina reads ?
Student 3 months ago, asked a question with at least 3 up-votes. For Best strategy for de novo assembly with illumina reads ?
Great Question 4 months ago, created a question with more than 5,000 views. For Coverage per contig from a BAM file
Popular Question 4 months ago, created a question with more than 1,000 views. For FASTA output in blast ?
Great Question 5 months ago, created a question with more than 5,000 views. For Coverage per contig from a BAM file
Popular Question 6 months ago, created a question with more than 1,000 views. For FASTA output in blast ?
Popular Question 7 months ago, created a question with more than 1,000 views. For FASTA output in blast ?
Great Question 8 months ago, created a question with more than 5,000 views. For RAxML outputs: which one I have to take ?
Popular Question 8 months ago, created a question with more than 1,000 views. For FASTA output in blast ?
Great Question 8 months ago, created a question with more than 5,000 views. For RAxML outputs: which one I have to take ?
Popular Question 9 months ago, created a question with more than 1,000 views. For FASTA output in blast ?
Popular Question 11 months ago, created a question with more than 1,000 views. For FASTA output in blast ?
Great Question 11 months ago, created a question with more than 5,000 views. For LD pruning and other QC before association analysis ?
Popular Question 12 months ago, created a question with more than 1,000 views. For FASTA output in blast ?
Popular Question 12 months ago, created a question with more than 1,000 views. For database for fungus ?
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Popular Question 14 months ago, created a question with more than 1,000 views. For FASTA output in blast ?
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