User: Gabe Rudy

gravatar for Gabe Rudy
Gabe Rudy300
Reputation:
300
Status:
Trusted
Location:
Golden Helix
Website:
http://blog.goldenheli...
Last seen:
2 months ago
Joined:
5 years, 8 months ago
Email:
r***@goldenhelix.com

about me

Posts by Gabe Rudy

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Copy number analysis by Golden Helix
... Hi there, I realize this question is old, but I found it when search and thought I would weigh in (I have worked on this algorithm at Golden Helix). 1) The Log2Ratio based segmentation can detected germline CNVs, but it really matters how you normalize the data from your microarrays. We have a ill ...
written 9 weeks ago by Gabe Rudy300
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Answer: A: GenomeBrowse stream network data
... From the GenomeBrowse main window, go to Add then click on the Url button on the left-hand side. You put in the base directory in the top line, and hit Enter. It will then list all available sources at that location. For example if you wanted to add: ftp://ftp-trace.ncbi.nih.gov:21/1000genomes/ft ...
written 3.7 years ago by Gabe Rudy300
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Answer: A: Refseqgene Directly To Gtf?
... I finally got an answer from Deanna Church on this in response to a blot post we wrote about variant annotation. Here is the GRCh37 GFF mappings of RefSeqGenes: ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz GFF3 can be a bit trick ...
written 4.5 years ago by Gabe Rudy300
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Refseqgene Directly To Gtf?
... UCSC says they take nighlty dumps of the mRNA sequences from RefSeqGens and BLAT them against their assemblies to generate the RefSeqGenes track. NCBI does have a mappings file on their FTP site: ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/RefSeqGene/GCF_000001405.25_refseqgene_alignments.gff3 But thi ...
gtf ncbi genes written 4.8 years ago by Gabe Rudy300
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Comment: C: New Human Genome Assembly (Grch38) Released
... "quite a long time" - https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/juXCCnNeyIM/discussion ...
written 4.8 years ago by Gabe Rudy300
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... Completely agree that there is under-appreciated complexity in different and (sometimes conflicting) representations used by different tools. My last point is simply this: 1-based coordinates are inadequate to describe variants as "features" as a pair of start/stop 1-based indexes (because of the i ...
written 5.1 years ago by Gabe Rudy300
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Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... I'm not sure your description of an insertion in 1-based coordinates is canonical. I'm actually not sure there is a canonical description of insertions in 1-based coordinate range, which is why many low-level tools prefer to work in 0-based coordinates. One of the primary advantages of 0-based coor ...
written 5.1 years ago by Gabe Rudy300
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Comment: C: How Does Genomebrowse Free Genome Browser From Golden Helix Compare?
... I really appreciate that response. People often over-estimate our size as a company and we do operate like a startup in the ways you mentioned (necessarily, as we are bootstrapped and have to be agile enough to survive in this market). Thanks for the feedback and keep it coming. ...
written 5.7 years ago by Gabe Rudy300
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Comment: C: How Does Genomebrowse Free Genome Browser From Golden Helix Compare?
... Since you posted this the event handling on Mac that caused the perceived slow responsiveness has been nagging me. I spent some time last Saturday night hacking on it and came up with away to compress the input events so we can be responsive and let the Mac do it's thing with the touch pad scroll ev ...
written 5.7 years ago by Gabe Rudy300
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Comment: C: How Does Genomebrowse Free Genome Browser From Golden Helix Compare?
... Ok, I can certainly agree you of all people should know what to expect. But thanks for letting me know you are using the track pad of a Mac to look through stuff. There are two issues that are hurting the performance there. One is we can't render as quickly on Mac. The drawing path just isn't as fa ...
written 5.7 years ago by Gabe Rudy300

Latest awards to Gabe Rudy

Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Refseqgene Directly To Gtf?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Refseqgene Directly To Gtf?
Appreciated 5.7 years ago, created a post with more than 5 votes. For A: How Does Genomebrowse Free Genome Browser From Golden Helix Compare?
Good Answer 5.7 years ago, created an answer that was upvoted at least 5 times. For A: How Does Genomebrowse Free Genome Browser From Golden Helix Compare?
Teacher 5.7 years ago, created an answer with at least 3 up-votes. For A: How Does Genomebrowse Free Genome Browser From Golden Helix Compare?

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