Moderator: Aaronquinlan

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Aaronquinlan10.0k
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http://quinlanlab.org/
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Posts by Aaronquinlan

<prev • 374 results • page 1 of 38 • next >
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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 5 months ago by Aaronquinlan10.0k
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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 17 months ago by Aaronquinlan10.0k
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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 18 months ago by Aaronquinlan10.0k
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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 20 months ago by Aaronquinlan10.0k • updated 20 months ago by Devon Ryan73k
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Answer: A: Intersect multiple BED files
... Have a look at this post: https://www.biostars.org/p/13516/ ...
written 22 months ago by Aaronquinlan10.0k
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Answer: A: bedtools genomecov .genome file usage
... With a BAM file, this is unnecssary. Sorry for the confusing docs. ...
written 2.7 years ago by Aaronquinlan10.0k
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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 2.8 years ago by Aaronquinlan10.0k
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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 2.8 years ago by Aaronquinlan10.0k
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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 2.8 years ago by Aaronquinlan10.0k
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Comment: C: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
... Also, GAT has been suggested as another approach that uses simulation: https://twitter.com/IlottNick/status/556104681135812608 ...
written 2.9 years ago by Aaronquinlan10.0k

Latest awards to Aaronquinlan

Appreciated 13 months ago, created a post with more than 5 votes. For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Appreciated 13 months ago, created a post with more than 5 votes. For A: Extract Sequences From Fasta Using Awk One-Liner
Appreciated 13 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 13 months ago, created a question with more than 5,000 views. For What Python Libraries Exist For Drawing Genes/Features/Intervals?
Popular Question 13 months ago, created a question with more than 1,000 views. For Job Postings
Teacher 13 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 15 months ago, created a post with more than 5 votes. For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Epic Question 15 months ago, created a question with more than 10,000 views. For What Ngs Read Simulators Are Available For Paired-End Data?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Calculation Of Average Mapping Quality Over A Given Genomic Region
Cylon 15 months ago, received 1,000 up votes.
Popular Question 17 months ago, created a question with more than 1,000 views. For Job Postings
Popular Question 17 months ago, created a question with more than 1,000 views. For Job Postings
Popular Question 18 months ago, created a question with more than 1,000 views. For Job Postings
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Calculation Of Average Mapping Quality Over A Given Genomic Region
Teacher 21 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?
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 2.0 years ago, created a post with more than 5 votes. For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Appreciated 2.1 years ago, created a post with more than 5 votes. For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Bedtools: Top N Most Similar Regions When Comparing Two Bed/Wig/Bam Files?
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
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Calculating Gc Content For All Ccds
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Job Postings
Appreciated 2.5 years ago, created a post with more than 5 votes. For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Good Question 2.5 years ago, asked a question that was upvoted at least 5 times. For Job Postings
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: How To Use Bedtools To Extract Promoters From A Mouse Bed File

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