User: Jonathanjacobs

gravatar for Jonathanjacobs
Reputation:
220
Status:
Trusted
Location:
Rockville, MD
Website:
http://microbe.land/
Twitter:
bioinformer
Scholar ID:
Google Scholar Page
Last seen:
1 day, 16 hours ago
Joined:
8 years, 7 months ago
Email:
j**************@gmail.com

I am currently Director of Global Product Development for Qiagen’s genomic and bioinformatics analysis portfolio. You can also catch up with me on Twitter (@bioinformer).  My professional interests include genomics-led research & discovery - especially in the microbial genomics arena, development of human and animal disease diagnostics, and mobilizing genomics systems for use in the field and at the point of care. 

Posts by Jonathanjacobs

<prev • 30 results • page 1 of 3 • next >
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Answer: A: CLCBio Genomics workbench - protein coding genes only
... Annika - you can use a track file of annotation types for your reference genome to mask out / in only what you want to see. Alternatively, you can subselect the expression table results to only those feature types ("CDS" types in this case) that you want to keep and then do all your downstream analy ...
written 5 days ago by Jonathanjacobs220
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Answer: A: How to check for contamination and separate the data?
... Using the latest version of CLC Genomics Workbench there are plenty of options for this 1. use the Microbial Genomics Module's binning tools to split your contigs from your assembly into bins either by taxonomic similarity or by sequence/kmer similarity (or both) - "pure bins" are probably good to ...
written 5 days ago by Jonathanjacobs220
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Answer: A: Export error WITH AGP?
... I know this is 2+ years old - but 1/ this may have been a bug at the time if you were trying to directly export a de novo assembly to FASTA. The work around was to first call consensus contigs from the assembly graph, and then export that. 2/ in the latest version (GxWB12 as of this writing) you ...
written 5 days ago by Jonathanjacobs220
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Answer: A: How do you interpret the results from GSEA analysis in CLC Genomics workbench?
... There are a number of ways to use GSEA analysis in CLC Genomics Workbench and Server - for RNAseq, miRNAseq, microarray analysis, and functional metagenomics profiling. In general, the CLC platform allows for Gene Ontology files to either be imported directly or directly downloaded (from GOC) and th ...
written 5 days ago by Jonathanjacobs220
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Comment: C: .clc to fastq
... Hi - just want to clarify on this point about not being able to recreate the data. IF the data was imported into CLC and the option to remove sequence read names, header info, etc was selected at the time of import - then yes the exact FASTQ would not be able to be recreated. However, you can alw ...
written 5 days ago by Jonathanjacobs220
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Answer: A: CLC Bio Variant detection with a Polyploid
... 2 is the correct answer. ;) ...
written 5 days ago by Jonathanjacobs220
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Answer: A: Results are now available for the precisionFDA CDRH Biothreat Challenge!
... I was happy we could participate and that we “placed”. I only wish I had known ahead of time we could have submitted more than one answer to the challenge. 😉😊 ...
written 7 months ago by Jonathanjacobs220
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Answer: A: Where can I find publicly available metagenomics contig datsets?
... I believe ENA and SRA have draft assemblies of MAGs - metagenomic assembled genomes - which is what you are looking for. I’m pretty sure all the MAGs (7000+) from the recent landmark paper from Parks et.al 2017 were deposited into Genbank under a single bioproject along with their predicted taxonomy ...
written 7 months ago by Jonathanjacobs220
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Comment: C: 97 Different Ways to do Metagenomics Classification...
... Thanks for the clarification. Also - here’s a direct link to the Zotero repo I have with the citations https://www.zotero.org/groups/2255187/microbial_genomics_references/items? (which i believe should include links to the articles and ability to download as bibtex, etc) ...
written 8 months ago by Jonathanjacobs220
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Blog: 97 Different Ways to do Metagenomics Classification...
... Hey all - I’ve notice a lot of people asking “how do i do X” wrt metagenomics or microbiome profiling. Or similarly- “Whats the best database / method / approach / etc?” for metagenomics. The reality is that it depends... on your specific research question, and on the underlying database you want / ...

Latest awards to Jonathanjacobs

Scholar 7 months ago, created an answer that has been accepted. For A: Where can I find publicly available metagenomics contig datsets?
Supporter 12 months ago, voted at least 25 times.
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: What Are These Rp11 'Genes' In The Genome?
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: Do You Feel Good Or Bad About Putting Your Photo At Biostar?
Autobiographer 5.8 years ago, has more than 80 characters in the information field of the user's profile.

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