User: Keith Callenberg

Reputation:
840
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Trusted
Location:
Pittsburgh, PA
Website:
http://www.calgorithms...
Twitter:
keithcallenberg
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Last seen:
8 hours ago
Joined:
6 years ago
Email:
k**************@gmail.com

Posts by Keith Callenberg

<prev • 85 results • page 1 of 9 • next >
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Answer: A: Bioinformatics in a clinical diagnostic setting versus research (academia)
... In clinical diagnostic labs, one important QC distinction is that controls with established known positive variants must be included on every sequencing run that includes one or more patient samples. If sufficient coverage and variant frequency for these variants can't be confirmed, the run must be ...
written 15 days ago by Keith Callenberg840
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Comment: C: How to analyze NGS data: An overview of nine different IT solutions
... I suspect you left company names out of this intentionally, but even after reading through the definitions I find it difficult to map real-world product/service examples to these categories. The categorization seems a bit too granular. If you had to give a label for your y-axis, what would you call ...
written 3 months ago by Keith Callenberg840
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Comment: C: Trimming adapter sequences - is it necessary?
... Since you (OP) are apparently part of ecSeq, John is taking the opportunity to point out that, at the bottom of the ecSeq page that you linked to, there is an illegal (as of 9/16/2016) usage of HighCharts. ...
written 4 months ago by Keith Callenberg840
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Answer: A: Variant calling for sanger reads
... It does not look to me like variant calling from .ab1 files has been implemented in any publicly-available R/Bioconductor packages. The one sanger popular sanger package will perform basecalling and alignment, but stops short of variant calling: https://www.bioconductor.org/packages/devel/bioc/vigne ...
written 5 months ago by Keith Callenberg840
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Comment: C: 23andme files uses GRCh37 or GRCh38 ?
... I can confirm this is currently the case by cross-referencing the coordinates in my raw 23andme data with dbSNP. (e.g. rs13096 is at coordinate 25359841, not 25206907) ...
written 7 months ago by Keith Callenberg840
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Comment: C: Number of SNPs by target sequencing
... Since a lot of the TruSight panels are designed for cancer, you might not be interested in all SNPs, but only cancer-related SNPs. If this is the case, you might want to use COSMIC instead: 1. Download the Illumina TruSight bed as Nicola mentions above. 2. Download the COSMIC coding mutations VCF ...
written 7 months ago by Keith Callenberg840
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Comment: C: How can I illustrate the importance of open source software in bioinformatics fo
... I have trouble even finding paid, closed-source packages for genomics. (That alone could be an argument.) But for example, I have seen people outside the field place higher value on packages like CLC Bio because the company "owns" and supports the tools contained within. ...
written 7 months ago by Keith Callenberg840
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Forum: How can I illustrate the importance of open source software in bioinformatics for people outside the field?
... I think it's safe to say that the majority of people in science, technology, and engineering fields are now comfortable with the idea of open source software. But this wasn't always the case, and there are still many people out there that are not comfortable with the idea of open source software bei ...
genome forum written 7 months ago by Keith Callenberg840 • updated 7 months ago by LLTommy570
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Answer: A: Is there a way to translate amino acid sequences into atomic sequences?
... Do you really want just an atomic sequence? Or are you asking for the molecular structure in 2D or 3D? In either case, you should keep in mind that back-translation (amino acid sequence to nucleotide sequence) will be ambiguous given that multiple codons code for each amino acid. You can use a too ...
written 9 months ago by Keith Callenberg840
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Answer: A: List Of Cloud Genomics Companies
... PierianDx offers end-to-end cloud-based analysis as well as just annotation/interpretation: http://pieriandx.com/technology/ ...
written 9 months ago by Keith Callenberg840

Latest awards to Keith Callenberg

Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Trimming adapter sequences - is it necessary?
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Trimming adapter sequences - is it necessary?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
Scholar 11 months ago, created an answer that has been accepted. For A: endoplasmic reticulum membrane size
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
Popular Question 18 months ago, created a question with more than 1,000 views. For Command-Line Tool For Swapping Amino Acid Side-Chain Rotamers
Scholar 21 months ago, created an answer that has been accepted. For A: endoplasmic reticulum membrane size
Student 23 months ago, asked a question with at least 3 up-votes. For Command-Line Tool For Swapping Amino Acid Side-Chain Rotamers
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
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Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
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Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates From Pdb File & Extracting The Region Of Interest
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