Moderator: Josh Herr

gravatar for Josh Herr
Josh Herr5.6k
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5,590
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Location:
University of Nebraska
Website:
http://joshuaherr.com/
Twitter:
@number_three
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Google Scholar Page
Last seen:
3 months, 1 week ago
Joined:
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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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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 3.2 years ago by Josh Herr5.6k
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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 3.2 years ago by Josh Herr5.6k
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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 3.2 years ago by Josh Herr5.6k
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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 3.2 years ago by Josh Herr5.6k
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Comment: C: comparison of species profiling simply using 16s rRNA in 16s rRNA amplicon seqeu
... Thank you!  I'm a little clearer on your question now.  I was unaware of these tools. ...
written 3.2 years ago by Josh Herr5.6k
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Comment: C: comparison of species profiling simply using 16s rRNA in 16s rRNA amplicon seqeu
... Thanks for the information -- would you mind posting the references (links?) about the mOTU tool and the use of the chaperone Cpn60 for species profiling?  I'm not familiar with either of these.  This may help others who have the same question you do with regards to this. Thanks again for your ques ...
written 3.2 years ago by Josh Herr5.6k
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Comment: C: comparison of species profiling simply using 16s rRNA in 16s rRNA amplicon seqeu
... No problem, it's my pleasure.  Just letting you know about S as being a Svedberg unit -- using the correct terminology will show that you understand concepts to other people. I'm unsure what you mean when you use "mOTU" here, which typically means "molecular operational taxonomic unit" which is arb ...
written 3.2 years ago by Josh Herr5.6k
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Answer: A: comparison of species profiling simply using 16s rRNA in 16s rRNA amplicon seqeu
... I'm not quite sure I fully understand your question -- maybe this is not obvious to you, but using markers for selective sequencing and random whole genome shotgun sequencing will not inherently capture the same sequences (or sequence diversity).  One is specific (16S) and the other is random (metag ...
written 3.2 years ago by Josh Herr5.6k
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Comment: C: Help in sff file format processing
... Great - Glad it worked out! ...
written 3.3 years ago by Josh Herr5.6k
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Comment: C: Help in sff file format processing
... Hello lzheng.chn I'm sorry to hear that you are having this problem -- I'm not sure what has caused it.  It might help if you add that sequence (AGAGCGAA) from all your samples to the oligo file that you provide in mothur to have that region trimmed during the shhh.flow step.   You can alternately ...
written 3.3 years ago by Josh Herr5.6k

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