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Old 01-28-2010, 04:41 PM   #1
quinlana
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Default BEDTools article

Hi,
A couple of folks had asked about how to cite BEDTools. The manuscript is now available in advanced access. We intended for it to be open access, but this has not yet happened.

http://bioinformatics.oxfordjournals...bstract/btq033

Aaron
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Old 01-28-2010, 04:42 PM   #2
lh3
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Congratulations!
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Old 01-29-2010, 04:05 AM   #3
quinlana
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Quote:
Originally Posted by lh3 View Post
Congratulations!
Thanks much, Heng! We've found combining samtools with bedtools to be incredibly useful for characterizing our results, eliminating alignment artifacts, and focusing on interesting regions. In other words, thank you for creating samtools.

Best,
Aaron
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Old 02-19-2010, 09:17 AM   #4
quinlana
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Default Version 2.5.3

Hi all,

I just posted version 2.5.3 of BEDTools which includes the following changes.

1. Fixed careless typo that disallowed "track" and "browser" lines.
2. Substantially increased the speed of pairToBed when comparing paired BAM alignments to BED annotations. The initial implementation left a bit to be desired; in some cases it is now up to 95% faster.
3. Fixed minor bug when reporting overlaps between BEDPE and BED features.
4. Fixed bug when using type "notboth" with BAM files in pairToBed.
5. When comparing BAM files to BED/GFF annotations with intersectBed or pairToBed, the __aligned__ sequence is used, rather than the __original__ sequence.
6. Fixed a bug in bamToBed when reporting edit distance from certain aligners.

http://bedtools.googlecode.com

Best,
Aaron


Quote:
Originally Posted by quinlana View Post
Hi,
A couple of folks had asked about how to cite BEDTools. The manuscript is now available in advanced access. We intended for it to be open access, but this has not yet happened.

http://bioinformatics.oxfordjournals...bstract/btq033

Aaron
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Old 03-03-2010, 07:50 AM   #5
ivang
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Default BEDTools. Documentation of intersectBed.

Hi Aaron and everybody,

The documentation of intersectBed nicely explains the use of -s and -f to mind strandedness and fraction overlapped. It is also clear that -v outputs records that do not overlap.

Two questions then:

1) When using -v, does intersectBed mind the fraction overlapped?

2) Assuming that 1) is affirmative, is this the correct syntax to catch only the records in A that do not overlap EXACTLY the records in B?

intersectBed -abam A.bam -b B.bed -s -f 1 -v > A_notexactly_B.bam

Thank you,

Ivan

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016
Fax: 1-301-496-9878
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Old 03-03-2010, 07:54 AM   #6
ivang
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Default

Sorry. I just realized that there is an official email list for BEDTools.

Ivan
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Old 03-03-2010, 08:53 AM   #7
quinlana
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Hi Ivan,

These are great questions --- I recognize the documentation could be better in this case. In fact, just yesterday I faced the same question for a similar analysis. In short, the answer to each of your questions is "yes".

An example with BED (not BAM), but the behavior is identical for BAM.

Code:
$ cat a.bed
chr1	10	100	a.small	90	+	
chr1	10	1000	a.large	900	-
Code:
$ cat b.bed
chr1	10	100	b.small	90	+
chr1	10	1000	b.large	900	+
Code:
$ intersectBed -a a.bed -b b.bed -f 1.0 -v
(NO OUTPUT)
Code:
$ intersectBed -a a.bed -b b.bed -f 1.0 -v -s
chr1	10	1000	a.large	900	-
Here's a link to the BEDTools Discussion list.

I hope this helps you out.
Best,
Aaron
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