Moderator: Josh Herr

gravatar for Josh Herr
Josh Herr5.5k
Reputation:
5,450
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Trusted
Location:
University of Nebraska
Website:
http://joshuaherr.com/
Twitter:
@number_three
Scholar ID:
Google Scholar Page
Last seen:
4 months ago
Joined:
6 years, 5 months ago
Email:
j************@gmail.com

I'm an assistant professor in the Department of Plant Pathology and The Center for Plant Science Innovation at the University of Nebraska.

You can read more about me and my interests at my blog Cyme & Cystidium or at my personal website or the website of my research lab.

You can also find me at Github, Software & Data Carpentry, and Twitter.

Posts by Josh Herr

<prev • 562 results • page 1 of 57 • next >
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Answer: C: Get phylogenetic tree from abundance table
... In addition to the other two answers, I'm going to chime in. I'm not being critical here, but it sounds like you are a little confused. It looks like what you show above is the taxonomy table from your OTU picking pipeline. This can be "made" into a phylogenetic tree, but you'll have to have your ...
written 5 months ago by Josh Herr5.5k
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Answer: A: Change maximum number of sequences on source code of ClaustalW
... I'm pretty sure you can run as much sequence data as possible through ClustalW, not that it has the memory to handle it. I do not see a flag for adjusting the memory of ClustalW. What have you tried? Have you tried to run all your data through ClustalW? You might be confined by your computer memor ...
written 8 months ago by Josh Herr5.5k
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Answer: A: Easy way to automatically save images of Krona HTML charts?
... I agree with the above answers as different tools selectively parse SVG in various ways. I have had good luck with [SVG Crowbar][1]. I then take the SVG output and use Illustrator or Inkscape to modify for publication. [1]: http://nytimes.github.io/svg-crowbar/ ...
written 10 months ago by Josh Herr5.5k
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Answer: A: Correcting for functional annotation database bias
... We recognize the bias and discuss it. I'm not aware of any efforts to account or quantify these biases yet. Much of our ability to understand this bias relies on laboratory validation and experiments to identify unknown functions, so we have a lot of work to do to fill in these gaps. ...
written 11 months ago by Josh Herr5.5k
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Comment: C: How to download raw sequence data from GEO/SRA
... Whoa!  How did I not know about prefetch - that is super handy.  Thanks for this tutorial. ...
written 23 months ago by Josh Herr5.5k
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Answer: A: Confirmation of metagenomic data
... 1) Does this sound reasonable, too strict, not strict enough? I'm a little thrown off by your question -- of course genomes from mixed samples are real genomes.  You're trying to establish standards with which to describe new species of viruses from metagenomic data.  There are already a lot of gro ...
written 2.1 years ago by Josh Herr5.5k
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Answer: A: Filtering BLAST results.
... This should be pretty straight forward as you should have your output in tabular format.  I do this quite frequently. 1. Sort on hits to your target genomes and output a list of the FASTA sequence headers. 2. Then I use a tool (the one I use is seqtk, but there are others) to input a list of these ...
written 2.1 years ago by Josh Herr5.5k
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Comment: A: Homology Analysis Tool - An analysis tool that can be used for both BLAST and RD
... No problem, didn't mean to be critical, just wanted to be clear and correct some issues with your wording and communication. I'm giving the tools a spin, thank you for your tool development and for letting us know about them! ...
written 2.2 years ago by Josh Herr5.5k
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Comment: C: Classify Metagenome Reads
... > is thare any way to reduce/improve the unclassified reads? The short answer: No.   We need better databases. ...
written 2.2 years ago by Josh Herr5.5k
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Comment: C: Homology Analysis Tool - An analysis tool that can be used for both BLAST and RD
... I haven't had a chance to use your BLAST/RDP GUI, but thanks for notifying us of the tool.   Not to be nitpicky, so excuse me for speaking up, but this is a major pet peeve of mine.  RDP classifier is used to identify ribosomal sequences from 16S primers, so I wouldn't call it a metagenomics tool a ...
written 2.2 years ago by Josh Herr5.5k

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