Moderator: Aaronquinlan
Aaronquinlan ♦ 11k
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Posts by Aaronquinlan
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... bedtools makewindows -b in.bed -w 1 ...
written 20 months ago by
Aaronquinlan ♦ 11k
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... 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 2.7 years ago by
Aaronquinlan ♦ 11k
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... 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 3.7 years ago by
Aaronquinlan ♦ 11k
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... [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 ...
written 3.7 years ago by
Aaronquinlan ♦ 11k
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... 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 4.0 years ago by
Aaronquinlan ♦ 11k
• updated
4.0 years ago by
Devon Ryan ♦ 94k
3
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Answer:
A: Intersect multiple BED files
... Have a look at this post: https://www.biostars.org/p/13516/ ...
written 4.1 years ago by
Aaronquinlan ♦ 11k
• updated
8 weeks ago by
RamRS ♦ 25k
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... With a BAM file, this is unnecssary. Sorry for the confusing docs.
...
written 5.0 years ago by
Aaronquinlan ♦ 11k
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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 5.0 years ago by
Aaronquinlan ♦ 11k
3
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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 5.0 years ago by
Aaronquinlan ♦ 11k
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... 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 5.0 years ago by
Aaronquinlan ♦ 11k
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For A: Extract Sequences From Fasta Using Awk One-Liner
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For A: Extract Sequences From Fasta Using Awk One-Liner
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For A: How To Filter Out Sequences With No Hits From Bwa Sam Output?
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For Introduction to bedtools.
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For What Python Libraries Exist For Drawing Genes/Features/Intervals?
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For What Ngs Read Simulators Are Available For Paired-End Data?
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For [Quinlan Lab] Postdoc or Staff Scientist in Rare Human Disease Research
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For A: Getting All Reads That Align To A Region In Compact Bed Format Using Bedtools?
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For Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
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For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
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For A: How To Filter Out Sequences With No Hits From Bwa Sam Output?
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For What Python Libraries Exist For Drawing Genes/Features/Intervals?
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For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
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For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
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For A: Calculation Of Average Mapping Quality Over A Given Genomic Region
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For A: Calculation Of Average Mapping Quality Over A Given Genomic Region
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