Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BED Tools forgenomic intervals

    Hi all,
    I recently completed a new suite of BED Tools for comparing, among other things, overlapping intervals of genomic features in UCSC BED format.

    Much of the functionality is analogous to that available on Galaxy's website. While I find Galaxy to be sublime, I much prefer doing such analyses on the command line, especially for large datasets such as those created by next-gen platforms.

    These tools allow one to answer questions such as:
    Which SNPs are in genes?
    How many Illumina reads align to repetitive elements?
    Which Segmental duplications overlap with CNVs?
    How many genes are within a 10kb window of each of my CNVs?
    What is the depth of sequencing coverage in my genome of interest?
    I want to merge overlapping features into a single interval.
    What intervals in the genome do not contain a repeat?

    They are available for 64-bit LINUX and Intel Macs at:


    Contact me if you have trouble or have feature requests. As time permits, I am happy to add new tools. The ones currently available were designed mainly for my needs, so I am certain I've neglected some obviously useful ones.

    Also, I plan to post the source code in the next few days, as it will be a much easier way of supporting all the various OS/Chip flavors. Plus, others can hack the code to suit their needs.

    All the best,
    Aaron
    Last edited by quinlana; 04-23-2009, 03:05 PM. Reason: typo; more info

  • #2
    Wow, thanks for making these available! I've been writing really hack versions of scripts to do a lot of this... so happy to have something more reliable!

    Comment


    • #3
      Source code now available.

      Hi all,
      I posted the source code for those that were having trouble with the available binaries. Installation instructions are now on the site as well as in the README you will download. I've also included some usage examples beyond what is on the website.



      Cheers.
      Aaron

      Comment


      • #4
        Version 1.2

        Hi all,
        Just a note to let you know that a new release of BEDTools is now available.

        What's new?

        1. closestBed. Return the feature in B that is closest to A. If multiple features in B overlap A, the one with the highest overlap is returned.
        2. windowBed. Added the ability to define separate windows for upstream and downstream overlaps.
        3. subtractBed. Remove the portion of A that is overlapped by features in B.
        4. linksBed. Creates an HTML file of intervals in a BED file. Handy for quickly navigating to interesting regions.

        Aaron
        Last edited by quinlana; 04-27-2009, 09:45 AM.

        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
        17 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        21 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        16 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        46 views
        0 likes
        Last Post seqadmin  
        Working...
        X