User: Lee Katz

gravatar for Lee Katz
Lee Katz2.8k
Reputation:
2,790
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Trusted
Location:
Atlanta, GA
Website:
http://leekatz.com/
Twitter:
lskatz
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Google Scholar Page
Last seen:
2 weeks, 1 day ago
Joined:
6 years, 9 months ago
Email:
l*****@gmail.com

I am a bioinformatics scientist at Centers for Disease Control and Prevention (CDC).  I am interested in evolution of bacterial pathogens including Vibrio and Listeria.  What I write here does not necessarily reflect the opinions or views of CDC.

Posts by Lee Katz

<prev • 365 results • page 1 of 37 • next >
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Answer: A: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
... Here is the code that actually works after I did some digging. It's a little bit of a hack but I don't believe it will cause any problems. Also I changed it to `Bio::FeatureIO` which I think is a little more mainstream. In this one-liner, `###` is printed to the output file after each input featu ...
written 10 months ago by Lee Katz2.8k
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Answer: A: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
... Jean-Karim is correct that the GFF module will probably only output features. However, you probably can manually write to the file in your perl script! There is a method called `$obj->fh` which returns the filehandle of your GFF object. Therefore you could write to the file as desired. For ex ...
written 10 months ago by Lee Katz2.8k
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Answer: A: Pfge Prediction Based On Wgs
... I was looking for this answer yet again but didn't see anything yet again, curiously. Here is the script I've developed over time for anyone else who might be looking. https://github.com/lskatz/lskScripts/blob/master/pfgeOnGenome.pl Run with --help for usage. ...
written 10 months ago by Lee Katz2.8k
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Comment: C: Portable genome browser
... I appreciate the idea @Jean, but @genomax2 is right that I would like to send something interactive over email. I can package and prepare something, but it needs to be ready to go when the recipient opens it from email. ...
written 10 months ago by Lee Katz2.8k
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Comment: C: Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
... Could you write an example of what you'd like to see in the GFF3 file? ...
written 10 months ago by Lee Katz2.8k
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Comment: C: Portable genome browser
... Unfortunately, running this and probably any other JS-based browser locally will trigger cross-site errors, as I have learned from Genoverse this morning. I thought that a JS-based client would be the optimal solution; however, there is a fundamental security obstacle. ...
written 10 months ago by Lee Katz2.8k
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Comment: C: Portable genome browser
... This is beautiful. I will try it out. ...
written 10 months ago by Lee Katz2.8k
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Comment: C: Portable genome browser
... No, I am not allowed to host a website at my work unfortunately, and I am ethically disinclined to redistribute IGV. The files have to go through email. ...
written 10 months ago by Lee Katz2.8k
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Comment: C: Portable genome browser
... I love IGV and use it; however it is not immediately clear how I could save a session complete with features and a reference assembly such that my colleagues could open the session from their email. I am also not clear how I'd zip all of IGV and send it over email when my size limit is 20MB and the ...
written 10 months ago by Lee Katz2.8k
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Comment: C: Portable genome browser
... My colleagues do not have IGV on their computers or anything similar. I think I'd like some self-extracting genome browser or something to work in a web browser when opened as an attachment. Another option is to have a hyperlink to some public website like UCSC or Galaxy that allows custom and pri ...
written 10 months ago by Lee Katz2.8k

Latest awards to Lee Katz

Popular Question 27 days ago, created a question with more than 1,000 views. For How Do I Convert 454 Ace To A Regular Ace?
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Commentator 9 months ago, created a comment with at least 3 up-votes. For C: How Much Does It Cost To Align A Flowcell In The Cloud?
Scholar 10 months ago, created an answer that has been accepted. For A: Multisample vcf to table
Popular Question 10 months ago, created a question with more than 1,000 views. For Minimum Spanning Tree
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Scholar 10 months ago, created an answer that has been accepted. For A: Multisample vcf to table
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Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How To Translate Old Parameters In New Version Of Blast 2.2.27 +
Popular Question 15 months ago, created a question with more than 1,000 views. For Multiple Sequence Alignment Score

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