Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.



    Aaron

  • #2
    Congratulations!

    Comment


    • #3
      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

      Comment


      • #4
        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.



        Best,
        Aaron


        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.



        Aaron

        Comment


        • #5
          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

          Comment


          • #6
            Sorry. I just realized that there is an official email list for BEDTools.

            Ivan

            Comment


            • #7
              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

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Current Approaches to Protein Sequencing
                by seqadmin


                Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
                04-04-2024, 04:25 PM
              • seqadmin
                Strategies for Sequencing Challenging Samples
                by seqadmin


                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                03-22-2024, 06:39 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 04-11-2024, 12:08 PM
              0 responses
              13 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-10-2024, 10:19 PM
              0 responses
              17 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-10-2024, 09:21 AM
              0 responses
              14 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-04-2024, 09:00 AM
              0 responses
              43 views
              0 likes
              Last Post seqadmin  
              Working...
              X