User: Keith Callenberg

Reputation:
860
Status:
Trusted
Location:
Pittsburgh, PA
Website:
http://www.calgorithms...
Twitter:
keithcallenberg
Scholar ID:
Google Scholar Page
Last seen:
3 days, 2 hours ago
Joined:
6 years, 4 months ago
Email:
k**************@gmail.com

Posts by Keith Callenberg

<prev • 86 results • page 1 of 9 • next >
0
votes
0
answers
156
views
0
answers
Comment: C: Download error 1000g2015aug for annovar
... I'm not seeing this error. Perhaps it is a network error on your side? Are you able to download other databases? ./annotate_variation.pl -buildver hg19 -downdb -webfrom annovar 1000g2015aug test NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: ...
written 3 months ago by Keith Callenberg860
2
votes
4
answers
480
views
4
answers
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 4 months ago by Keith Callenberg860
3
votes
1
answer
467
views
1
answers
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 7 months ago by Keith Callenberg860
4
votes
4
answers
3.7k
views
4
answers
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 8 months ago by Keith Callenberg860
0
votes
2
answers
410
views
2
answers
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 9 months ago by Keith Callenberg860
1
vote
1
answer
379
views
1
answers
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 11 months ago by Keith Callenberg860
1
vote
1
answer
411
views
1
answers
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 11 months ago by Keith Callenberg860
1
vote
3
answers
699
views
3
answers
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 11 months ago by Keith Callenberg860
10
votes
3
answers
699
views
3
answers
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 11 months ago by Keith Callenberg860 • updated 11 months ago by LLTommy850
0
votes
3
answers
584
views
3
answers
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 13 months ago by Keith Callenberg860

Latest awards to Keith Callenberg

Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Trimming adapter sequences - is it necessary?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Trimming adapter sequences - is it necessary?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
Scholar 15 months ago, created an answer that has been accepted. For A: endoplasmic reticulum membrane size
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
Popular Question 22 months ago, created a question with more than 1,000 views. For Command-Line Tool For Swapping Amino Acid Side-Chain Rotamers
Scholar 2.1 years ago, created an answer that has been accepted. For A: endoplasmic reticulum membrane size
Student 2.2 years ago, asked a question with at least 3 up-votes. For Command-Line Tool For Swapping Amino Acid Side-Chain Rotamers
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
Voter 3.2 years ago, voted more than 100 times.
Supporter 3.2 years ago, voted at least 25 times.
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Software For Hydrogen Bond Detection In Pdb Data?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Best Graphic For Homology Modeling?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Extracting Coordinates From Pdb File & Extracting The Region Of Interest
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Protein 3D Structure Principal Axes
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: What Wetlab Techniques Does A Bioinformatician Need To Be Able To Perform, If An
Student 3.2 years ago, asked a question with at least 3 up-votes. For Command-Line Tool For Swapping Amino Acid Side-Chain Rotamers
Autobiographer 3.2 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 574 users visited in the last hour