User: joneill4x

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joneill4x10
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New User
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Canada
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4 months ago
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3 years ago
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Posts by joneill4x

<prev • 17 results • page 1 of 2 • next >
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Answer: A: How To Get The Subclusters From The Object Of Hclust() Using Cutree() According
... Thank you, this was really helpful. EDIT: this was meant to be under seidel's answer. ...
written 4 months ago by joneill4x10
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unitigs for proovread
... "Unitigs are high-confidence assembly fragments produced by for example ALLPATHS, Meraculous2 or the Celera Assembler. In contrast to contigs, unitigs don’t extend past any conflict in the underlying short read data, making them highly reliable." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4609002/ ...
proovread illumina idba_ud written 21 months ago by joneill4x10
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Comment: C: Newbler 3 assembler download - assembly of highly heterozygous genome
... Hi lexnederbragt, thanks for your answer. I tried using that link again just now, but it still is showing only v2.9 available for download. ...
written 21 months ago by joneill4x10
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Newbler 3 assembler download - assembly of highly heterozygous genome
... Hello all, Does anyone know where I can obtain a copy of the Newbler v3.0 assembler? I have managed to download and install v2.9, having obtained it from from the 454 official website. Link: http://454.com/contact-us/software-request.asp However, v2.9 has a max read length of 2000, while v3.0 ...
newbler assembly written 22 months ago by joneill4x10 • updated 3 months ago by salgado70
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Comment: C: Detecting gene duplication in de-novo assembly
... OK! I'll give that a try. Thanks Wouter! ...
written 2.1 years ago by joneill4x10
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Comment: C: Detecting gene duplication in de-novo assembly
... RDXplorer looks like a good one for me to try. Edit - only for human genome, looks like I can't use it. ...
written 2.1 years ago by joneill4x10
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Comment: C: Detecting gene duplication in de-novo assembly
... Diploid genome, Heterozygous rate 0.01 - 0.02. Estimated genome size 700 000 000 bases. ~15X PacBio ~65X Illumina coverage ...
written 2.1 years ago by joneill4x10
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Comment: C: Detecting gene duplication in de-novo assembly
... Thanks Igor. I noticed that a lot of those tools require multiple samples in order to detect CNV. In my case, I only have reads (PE miseq, PE hiseq, and PacBio) and a de-novo assembly. So my problem is a little different than the typical CNV detection it seems. ...
written 2.1 years ago by joneill4x10
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Detecting gene duplication in de-novo assembly
... I have recently assembled a genome de-novo. I am looking for fertility genes where there is only 1 copy of the gene in the true genome. I am worried that if there are multiple copies of a gene in the true genome, they will appear as a single gene in the de-novo assembly. Is this a reasonable conc ...
genome gene next-gen sequencing written 2.1 years ago by joneill4x10
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Comment: C: De novo genome assembly strategy
... I found SPAdes and dipSPAdes to run extremely slow when using PacBio reads as input. ...
written 2.1 years ago by joneill4x10

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Popular Question 13 months ago, created a question with more than 1,000 views. For De novo genome assembly strategy
Popular Question 20 months ago, created a question with more than 1,000 views. For De novo genome assembly strategy

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