Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BEDTools Version 2.7

    Hi all,
    I just posted the new version of BEDTools. This was also posted on the BEDTools mailing list, so my apologies to those that were struck twice or thrice.



    Below are the most relevant release notes.
    Best,
    Aaron


    General:

    -- "Gzipped" BED and GFF files are now supported as input by all BEDTools. Such files must end in ".gz".
    -- Tools that process BAM alignments now uniformly (and properly) compute an ungapped alignment end position based on the BAM CIGAR string. Specifically, "M", "D" and "N" operations are observed when computing the end position.
    -- bamToBed requires the BAM file to be sorted/grouped by read id when creating BEDPE output. Note that this is the typical order in which most aligners create SAM/BAM output. This requirement allows the alignment end coordinate for each end of the pair to be properly computed based on its CIGAR string. The same requirement applies to pairToBed.
    -- I finally updated the manual.
    -- Many unseen modifications to the code that improve clarity and sanity-checking and facilitate future additions/modifications.


    New Tool:
    -- bedToBam. This utility will converts BED files to BAM format. Both "blocked" (aka BED12) and "unblocked" (e.g. BED6) formats are acceptable. This allows one to, for example, compress large BED files such as dbSNP into BAM format for efficient visualization with IGV, Gambit, and Tablet.


    Changes to existing tools:
    -- intersectBed
    1. Added -wao option to report 0 overlap for features in A that do not intersect any features in B. This is an extension of the -wo option released in v2.6.1.
    -- bamToBed
    1. Requires that BAM input be sorted/grouped by read name.
    -- pairToBed
    1. Requires that BAM input be sorted/grouped by read name.
    2. Allows use of minimum mapping quality or total edit distance for score field.
    -- windowBed
    1. Now supports BAM input.
    -- genomeCoverageBed
    1. -bga option. Allows blocks of zero coverage to be reported in BEDGRAPH format.
    2. Eliminated potential seg fault.

  • #2
    RNA-seq ambiguous reads

    Hi Aaron
    I have done RNA-seq on maize endopserms. I would like to know how does coverageBed handle "ambiguous reads" in RNA-seq experiments? Is there a separate entry that lists such ambiguous reads? I see, in my RNA-seq data, many reads matching mutiple features. Occasionally I also see mRNA reads matching introns. The GFF annotation for maize is not accurate. In addition maize is chock full of retrotransposons that transcribe through various intermediates.

    Siva

    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, 07-16-2024, 05:49 AM
    0 responses
    22 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-15-2024, 06:53 AM
    0 responses
    30 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-10-2024, 07:30 AM
    0 responses
    40 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 09:45 AM
    0 responses
    205 views
    0 likes
    Last Post seqadmin  
    Working...
    X