Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Median basepair coverage of reads across contig length

    Hello experts,

    I am having hard time to understand a method from a metagenomic paper. The author used "median basepair coverage of reads across contig length" to measure base pair coverage of contigs. Does this mean that reads were aligned to contigs and length of contigs covered by reads were used? What does median mean here? Could anyone give me more detailed explanation on this? Any advice would be greatly appreciated.
    Last edited by morning latte; 12-22-2014, 07:07 AM.

  • #2
    Perhaps if you give us a reference to the paper then we could figure out what the author meant.

    As a wild guess since this is metagenomics thus implying multiple read sets aligned to each contig, I think that (1) the reads were aligned and (2) a coverage per contig per read set was obtained and then (3) a median per contig was found for all of the read sets. But as I say that an wild guess.

    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, 07-10-2024, 07:30 AM
    0 responses
    23 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 09:45 AM
    0 responses
    201 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 08:54 AM
    0 responses
    209 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-02-2024, 03:00 PM
    0 responses
    192 views
    0 likes
    Last Post seqadmin  
    Working...
    X