Moderator: Josh Herr

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Josh Herr5.5k
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Location:
University of Nebraska
Website:
http://joshuaherr.com/
Twitter:
@number_three
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Last seen:
3 weeks ago
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7 years, 1 month 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

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Benchmarking single SNP mapping
... I've come up with a homework exercise for my class on SNP mapping and benchmarking. The comical part is I can't figure out why I am not mapping the SNP myself. I'm not a novice at this anymore, but I'm banging my head against the wall to get this to work. For the exercise, I have taken a 13,000 bp ...
snps bowtie wgsim bwa mapping written 22 days ago by Josh Herr5.5k • updated 10 days ago by Biostar ♦♦ 20
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Comment: C: Relabel/rename OTU IDs in an OTU table using a taxonomy file
... This should be a pretty easy conversion. Do you mind updating the text in your question to show what you have exactly and what is your desired formatted output? There are lots of ways using [biom-format][1] to add taxonomy to an OTU table, but what you might want to be done could also be done easi ...
written 12 weeks ago by Josh Herr5.5k
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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 13 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 16 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 18 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 19 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 2.5 years 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 2.8 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 2.8 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 2.8 years ago by Josh Herr5.5k

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