Moderator: Aaronquinlan
Aaronquinlan ♦ 11k
- Reputation:
- 10,860
- Status:
- Trusted
- Location:
- United States
- Website:
- http://quinlanlab.org/
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 year, 11 months ago
- Joined:
- 10 years, 1 month ago
- Email:
- a***********@gmail.com
Posts by Aaronquinlan
<prev
• 375 results •
page 1 of 38 •
next >
1
vote
5
answers
832
views
5
answers
... bedtools makewindows -b in.bed -w 1 ...
written 2.1 years ago by
Aaronquinlan ♦ 11k
1
vote
3
answers
1.9k
views
3
answers
... 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 3.1 years ago by
Aaronquinlan ♦ 11k
0
votes
0
answers
1.5k
views
0
answers
... 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 4.1 years ago by
Aaronquinlan ♦ 11k
7
votes
0
answers
1.5k
views
0
answers
... [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 4.1 years ago by
Aaronquinlan ♦ 11k
2
votes
3
answers
2.5k
views
3
answers
... 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 4.4 years ago by
Aaronquinlan ♦ 11k
• updated
4.4 years ago by
Devon Ryan ♦ 96k
3
votes
4
answers
3.7k
views
4
answers
Answer:
A: Intersect multiple BED files
... Have a look at this post: https://www.biostars.org/p/13516/ ...
written 4.5 years ago by
Aaronquinlan ♦ 11k
• updated
6 months ago by
RamRS ♦ 27k
4
votes
2
answers
4.4k
views
2
answers
... With a BAM file, this is unnecssary. Sorry for the confusing docs.
...
written 5.4 years ago by
Aaronquinlan ♦ 11k
1
vote
1
answer
1.3k
views
1
answers
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 5.4 years ago by
Aaronquinlan ♦ 11k
3
votes
1
answer
1.3k
views
1
answers
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 5.4 years ago by
Aaronquinlan ♦ 11k
5
votes
2
answers
3.2k
views
2
answers
... 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 5.4 years ago by
Aaronquinlan ♦ 11k
Latest awards to Aaronquinlan
Good Answer
2.0 years ago,
created an answer that was upvoted at least 5 times.
For A: Extract Sequences From Fasta Using Awk One-Liner
Appreciated
3.1 years ago,
created a post with more than 5 votes.
For A: Extract Sequences From Fasta Using Awk One-Liner
Appreciated
3.1 years ago,
created a post with more than 5 votes.
For A: How To Filter Out Sequences With No Hits From Bwa Sam Output?
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Introduction to bedtools.
Great Question
3.1 years ago,
created a question with more than 5,000 views.
For What Python Libraries Exist For Drawing Genes/Features/Intervals?
Prophet
3.1 years ago,
created a post with more than 20 followers.
For What Ngs Read Simulators Are Available For Paired-End Data?
Good Answer
3.1 years ago,
created an answer that was upvoted at least 5 times.
For A: Extract Sequences From Fasta Using Awk One-Liner
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For [Quinlan Lab] Postdoc or Staff Scientist in Rare Human Disease Research
Teacher
3.1 years 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?
Great Question
3.1 years ago,
created a question with more than 5,000 views.
For Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
Appreciated
3.1 years ago,
created a post with more than 5 votes.
For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Appreciated
3.7 years ago,
created a post with more than 5 votes.
For A: How To Filter Out Sequences With No Hits From Bwa Sam Output?
Appreciated
3.7 years ago,
created a post with more than 5 votes.
For A: Extract Sequences From Fasta Using Awk One-Liner
Great Question
3.7 years ago,
created a question with more than 5,000 views.
For What Python Libraries Exist For Drawing Genes/Features/Intervals?
Appreciated
3.7 years ago,
created a post with more than 5 votes.
For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Teacher
3.7 years 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
3.9 years ago,
created a post with more than 5 votes.
For C: Additional Data In Human Genome (Hg18 / Hg19) Assembly ?
Epic Question
3.9 years ago,
created a question with more than 10,000 views.
For What Ngs Read Simulators Are Available For Paired-End Data?
Cylon
3.9 years ago,
received 1,000 up votes.
Good Answer
3.9 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
4.1 years ago,
created an answer that was upvoted at least 5 times.
For A: Calculation Of Average Mapping Quality Over A Given Genomic Region
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2001 users visited in the last hour