Moderator: Aaronquinlan

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Aaronquinlan10k
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United States
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http://quinlanlab.org/
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1 month, 4 weeks ago
Joined:
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Posts by Aaronquinlan

<prev • 375 results • page 1 of 38 • next >
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Answer: A: Expanding Genomic Coordinates Using Bedtools
... bedtools makewindows -b in.bed -w 1 ...
written 12 weeks ago by Aaronquinlan10k
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Answer: A: how to randomly select intervals of different lengths (not records) from a BED f
... The problem is that when your input BED record is not evenly divisible by L, you will have one final interval whose length is L. Just use awk to filter those out. Let's pretend we want 5 randomly chose intervals of length 10: > bedtools makewindows -b set.bed -w 10 \ | awk '($3-$2) ...
written 15 months ago by Aaronquinlan10k
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Comment: C: [Quinlan Lab] Postdoctoral Fellow in Rare Human Disease Research
... This position is still available and we are eager to fill it. It need not be filled as a postdoctoral position - staff scientist / analyst positions would also be considered. Pay is competitive, the department and lab are thriving, and the location is phenomenal. ...
written 2.3 years ago by Aaronquinlan10k
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Job: [Quinlan Lab] Postdoc or Staff Scientist in Rare Human Disease Research
... [The Quinlan Laboratory][1] in the [Department of Human Genetics][2] at the University of Utah is looking to hire a talented postdoctoral scientist or staff scientist who has a passion for genomics and the study of human disease. This scientist will lead the application and development of computatio ...
genetics disease job human rare written 2.3 years ago by Aaronquinlan10k
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Answer: A: coverageBed: what am I doing wrong?
... Thanks very much for reporting this. I have pushed a fix to the bedtools repository. It will be a part of the next release, but you can always update your code now by cloning from the repository. Below is an updated plot based upon the following command: $ bedtools coverage -a features.bed -b ...
written 2.5 years ago by Aaronquinlan10k • updated 2.5 years ago by Devon Ryan84k
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Answer: A: Intersect multiple BED files
... Have a look at this post: https://www.biostars.org/p/13516/ ...
written 2.7 years ago by Aaronquinlan10k
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Answer: A: bedtools genomecov .genome file usage
... With a BAM file, this is unnecssary. Sorry for the confusing docs. ...
written 3.6 years ago by Aaronquinlan10k
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Comment: C: bedtools probelm of syntax
... Yep, default (without providing -f) will detect one base pair.  If you use, -f you are trying to override that default, and as such, must provide a value to use as the override. -f Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). ...
written 3.6 years ago by Aaronquinlan10k
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Answer: A: bedtools probelm of syntax
... You need to supply a value for the -f argument.  For example, if you require 50% overlap, provide "-f 0.05". ...
written 3.6 years ago by Aaronquinlan10k
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Answer: A: Does multiIntersectBed works with -u and -f parameter?
... You can't do this directly with bedtools multiinter, but you can answer this by combing a few tools. It is a smidge complicated, but it should work and it demonstrates how combining multiple bedtools can usually get you the answer you need.  ➜ cat a.bed chr1 15 20 a1 chr1 1 ...
written 3.6 years ago by Aaronquinlan10k

Latest awards to Aaronquinlan

Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: Extract Sequences From Fasta Using Awk One-Liner
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Getting All Reads That Align To A Region In Compact Bed Format Using Bedtools?
Popular Question 15 months ago, created a question with more than 1,000 views. For Introduction to bedtools.
Popular Question 15 months ago, created a question with more than 1,000 views. For [Quinlan Lab] Postdoc or Staff Scientist in Rare Human Disease Research
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Extract Sequences From Fasta Using Awk One-Liner
Prophet 15 months ago, created a post with more than 20 followers. For What Ngs Read Simulators Are Available For Paired-End Data?
Great Question 15 months ago, created a question with more than 5,000 views. For What Python Libraries Exist For Drawing Genes/Features/Intervals?
Great Question 15 months ago, created a question with more than 5,000 views. For Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
Appreciated 15 months ago, created a post with more than 5 votes. For A: How To Filter Out Sequences With No Hits From Bwa Sam Output?
Appreciated 15 months ago, created a post with more than 5 votes. For A: Extract Sequences From Fasta Using Awk One-Liner
Appreciated 15 months ago, created a post with more than 5 votes. For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Appreciated 23 months ago, created a post with more than 5 votes. For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Appreciated 23 months ago, created a post with more than 5 votes. For A: Extract Sequences From Fasta Using Awk One-Liner
Appreciated 23 months ago, created a post with more than 5 votes. For A: How To Filter Out Sequences With No Hits From Bwa Sam Output?
Great Question 23 months ago, created a question with more than 5,000 views. For What Python Libraries Exist For Drawing Genes/Features/Intervals?
Popular Question 23 months ago, created a question with more than 1,000 views. For Job Postings
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Getting All Reads That Align To A Region In Compact Bed Format Using Bedtools?
Appreciated 2.1 years ago, created a post with more than 5 votes. For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Epic Question 2.1 years ago, created a question with more than 10,000 views. For What Ngs Read Simulators Are Available For Paired-End Data?
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Calculation Of Average Mapping Quality Over A Given Genomic Region
Cylon 2.1 years ago, received 1,000 up votes.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Job Postings
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Job Postings
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Job Postings
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Calculation Of Average Mapping Quality Over A Given Genomic Region

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