User: Jonathanjacobs

gravatar for Jonathanjacobs
Reputation:
240
Status:
Trusted
Location:
Rockville, MD
Website:
http://microbe.land/
Twitter:
bioinformer
Scholar ID:
Google Scholar Page
Last seen:
2 months, 2 weeks ago
Joined:
8 years, 11 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 • 36 results • page 1 of 4 • next >
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Answer: A: Which aligner is best suited for circular human mitochondrial genome?
... CLC Genomics Workbench's read mapper works with circularized references and will map reads across origin without any issue. ...
written 10 weeks ago by Jonathanjacobs240
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Answer: A: Circular Genome Alignment
... FWIW - CLC Genomics Workbench's read mapper supports circularized reference genomes and will map reads across origins without any issue. ...
written 10 weeks ago by Jonathanjacobs240
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Comment: C: Aligning Circular Sequences
... Just as an FYI - This is actually not the case with CLC. The CLC read mapper, aligner, and multiple sequence alignment tools indeed support aligning circularized sequences or (in the case of read mapping NGS data) correctly mapping to a circular reference. In addition - the ability to set fixpoints ...
written 10 weeks ago by Jonathanjacobs240
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Answer: A: aligning to circular sequence
... I know this is an old post - but I wanted to clarify that CLC Genomics Workbench **does indeed support mapping reads to circular references**. The issue is that (currently) our track **viewer** is only linear - something we plan to improve on in 2020 as a number of customers have requested CIRCOS li ...
written 10 weeks ago by Jonathanjacobs240
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Answer: A: CLC not outputting or showing table from Fisher's Exact Test
... Jjrin - which version of CLC GxWB and B2G are you using? For help with CLC specifically - please reach out to QIAGEN's bioinformatics support team at ts-bioinformatics@qiagen.com Blast2Go is a third party plugin developed by BioBam using the CLC API. For help with that, you should contact their s ...
written 3 months ago by Jonathanjacobs240
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Comment: C: Tracing back files used in CLC Genomics?
... 👍👍 And any of the output files from your analysis should have links to the original input files in the history tab. (Assuming they weren’t deleted or something) if your click them it will jump you to where the files are in the nav window ...
written 3 months ago by Jonathanjacobs240
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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 4 months ago by Jonathanjacobs240
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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 4 months ago by Jonathanjacobs240
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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 4 months ago by Jonathanjacobs240
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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 4 months ago by Jonathanjacobs240

Latest awards to Jonathanjacobs

Scholar 11 months ago, created an answer that has been accepted. For A: Where can I find publicly available metagenomics contig datsets?
Supporter 16 months ago, voted at least 25 times.
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: What Are These Rp11 'Genes' In The Genome?
Teacher 6.2 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?
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