BEDTools article

quinlana · 01-28-2010, 05:41 PM

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

lh3 · 01-28-2010, 05:42 PM

Congratulations!

quinlana · 01-29-2010, 05:05 AM

Quote:

Originally Posted by lh3

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

quinlana · 02-19-2010, 10:17 AM

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

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

ivang · 03-03-2010, 08:50 AM

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

ivang · 03-03-2010, 08:54 AM

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

Ivan

quinlana · 03-03-2010, 09:53 AM

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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01-28-2010, 05:41 PM	#1
quinlana Senior Member Location: Charlottesville Join Date: Sep 2008 Posts: 119	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

03-03-2010, 08:50 AM	#5
ivang Junior Member Location: Washington DC. (US) Join Date: May 2009 Posts: 2	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

03-03-2010, 09:53 AM	#7
quinlana Senior Member Location: Charlottesville Join Date: Sep 2008 Posts: 119	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

01-28-2010, 05:42 PM	#2
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 693	Congratulations!

03-03-2010, 08:54 AM	#6
ivang Junior Member Location: Washington DC. (US) Join Date: May 2009 Posts: 2	Sorry. I just realized that there is an official email list for BEDTools. Ivan