User: John St. John

gravatar for John St. John
John St. John1.1k
Reputation:
1,090
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Location:
San Francisco, CA, Cancer Therapeutics Innovation Group
Website:
http://www.johnstjohn....
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Google Scholar Page
Last seen:
5 days, 22 hours ago
Joined:
7 years, 5 months ago
Email:
j***************@gmail.com

I am a Bioinformatics Analyst at Cancer Therapeutics Innovation Group.

Posts by John St. John

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Reporting p.value for my PCA results
... Actually you can get p-values for the number of principal components. There has been some recent work on this. Unfortunately I have not seen it implemented in any PCA implementations that I use :( https://projecteuclid.org/download/pdfview_1/euclid.aos/1513328584 ...
written 24 days ago by John St. John1.1k
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Absolute/Hapseg on Exome (WES) Data?
... I have recently gotten Absolute working with whole exome sequencing data, but I really wanted to use the information present in phasing allele specific copy number ratios that Hapseg gives to help out with the identifiably problem (multiple similar solutions, for example see http://bioinformatics.ox ...
exome absolute hapseg next-gen tumor purity written 4.6 years ago by John St. John1.1k • updated 3.2 years ago by wangjq0
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Comment: C: How Do Heterozygotes And Somatic Mutations Manifest In Sequencing Projects
... One bit that may or may not concern you. CCF is not an accurate term for what this number means. Kind of an issue in a lot of these papers. What the number really means is the average number of mutations per cell. This usually doesn't matter, but consider the example where you start with a mutation, ...
written 4.6 years ago by John St. John1.1k
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Comment: C: How Do Heterozygotes And Somatic Mutations Manifest In Sequencing Projects
... Also incase anyone is wondering (took me a minute to notice this) the figure is showing the case where you literally have 3 cells, two are tumor and one is normal. So the purity of .67 is a rounded version of 2/3 in their example. If you do more sig-figs on the purity you get closer to 0.5 using you ...
written 4.6 years ago by John St. John1.1k
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Comment: C: Displaying Different Sized Lines In Ucsc Genome Browser
... Yea, not sure if you can do this in custom tracks or not. Try right clicking on one of the default tracks, you should see an option "Configure ..." near the bottom of the drop down that comes up when you do that. Just tried this. ...
written 5.4 years ago by John St. John1.1k
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Answer: A: Human Exome Capture Library Coordinates Download
... I was told recently by Agilent to download the data from here https://earray.chem.agilent.com/suredesign Just create an account, log in, and select the "Find Designs" tab, then under that select "Agilent Catalog", then there should be a list of the different SureSelect related bed files and whatno ...
written 5.5 years ago by John St. John1.1k
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Answer: A: Normalization Procedure For The Rna-Seq Data Based On Counts
... You could always load the data into an R matrix and then apply whatever normalization technique you want (eg mean, upper quartile, median, whatever else). ...
written 5.6 years ago by John St. John1.1k
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Answer: A: Dbsnp132 1000Genomes Vcf File Info Field: Bitfield Structure
... Ok I deserve some props. I think I got this to work in python without the need for bitshifting. The trick is that you need to first convert the hex string in the VP=... field into *bytes, which involves two hex characters at a time. Next I noticed that although the bytes are arranged and read left ...
written 5.6 years ago by John St. John1.1k
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Comment: C: Dbsnp132 1000Genomes Vcf File Info Field: Bitfield Structure
... Here is an up-to-date link for snp_bitfield_2.cpp: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objtools/snputil/snp_bitfield_2.cpp ...
written 5.6 years ago by John St. John1.1k
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Comment: C: Genome Music Path-Scan Negative P-Value?
... Thanks for digging up that post for me! ...
written 5.6 years ago by John St. John1.1k

Latest awards to John St. John

Great Question 2.6 years ago, created a question with more than 5,000 views. For Mapping From Gene Names To Gene Lengths In R?
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Has Anyone Successfully Used Allpaths-Lg On A >500Mb Genome With The Minimal Sho
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Generating Genome Base Qualities From A Bam Alignment?
Guru 2.6 years ago, received more than 100 upvotes.
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Considering Bachelor Options, Need Something To Introduce Me To Real World Bioin
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Why Are There Many Rna-Seq Hits To Intronic Regions?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Genome Music Path-Scan Negative P-Value?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Absolute/Hapseg on Exome (WES) Data?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Identify Contamination With Blast
Commentator 3.4 years ago, created a comment with at least 3 up-votes. For C: How Do Heterozygotes And Somatic Mutations Manifest In Sequencing Projects
Appreciated 4.3 years ago, created a post with more than 5 votes. For A: Extract Sub_Tree From Big Phylogeny
Appreciated 4.3 years ago, created a post with more than 5 votes. For A: Why Are There Many Rna-Seq Hits To Intronic Regions?
Good Answer 4.3 years ago, created an answer that was upvoted at least 5 times. For A: Extract Sub_Tree From Big Phylogeny
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Set Up Soapdenovo (Or Just A Fasta File Of Scaffolds) For Ncbi Wgs Genome Submission
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Mapping From Gene Names To Gene Lengths In R?
Student 4.3 years ago, asked a question with at least 3 up-votes. For Identify Contamination With Blast
Appreciated 4.9 years ago, created a post with more than 5 votes. For A: Out Of Disk Space With Picard Tools ?
Appreciated 4.9 years ago, created a post with more than 5 votes. For A: Extract Sub_Tree From Big Phylogeny
Good Answer 4.9 years ago, created an answer that was upvoted at least 5 times. For A: Out Of Disk Space With Picard Tools ?
Good Answer 4.9 years ago, created an answer that was upvoted at least 5 times. For A: Extract Sub_Tree From Big Phylogeny
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Human Exome Capture Library Coordinates Download
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Ion Torrent Mapping
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Why Are There Many Rna-Seq Hits To Intronic Regions?
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Considering Bachelor Options, Need Something To Introduce Me To Real World Bioin

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