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
          Exploring the Dynamics of the Tumor Microenvironment
          by seqadmin




          The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
          07-08-2024, 03:19 PM
        • seqadmin
          Exploring Human Diversity Through Large-Scale Omics
          by seqadmin


          In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
          06-25-2024, 06:43 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 07:20 AM
        0 responses
        24 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-16-2024, 05:49 AM
        0 responses
        38 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-15-2024, 06:53 AM
        0 responses
        44 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-10-2024, 07:30 AM
        0 responses
        41 views
        0 likes
        Last Post seqadmin  
        Working...
        X