Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • using khist to generate kmer coverage histogram

    I used khist from bbmap to generate kmer coverage, the attached included the output and the log file. There are a few things I am not very clear. what's different between "Raw count and unique_kmer" in the output file?
    Is "unique kmer" defined as "the kmer only appear once in the dataset"? what's the differences between unique kmer and the kmers whose depth is one?
    When I plot the dataset for coverage, which column should I use? raw count or unique kmer?

    The data is a metagenome data.

    Thanks
    Attached Files

  • #2
    The program (conceptually) allocates one counter per kmer, and increments it every time that kmer is seen. So, let's say K=2 and the input string is "CATTATTT".

    That breaks down into these kmers:
    CA, AT, TT, TA, AT, TT, TT

    After reverse-complementing to store only a single canonical copy, either forward or reverse, we get this:

    CA, AT, AA, AT, AT, AA, AA

    So the kmer counts stored by the program would be:

    AA: 3
    AT: 3
    CA: 1

    This would equate to 3 unique kmers. The histogram would look like this:
    Code:
    #Depth	Raw_Count	Unique_Kmers
    1	1	1
    3	6	2
    Generally, (column 3) = (column 2)/(column 1).

    So line 1 means there was a single kmer (CA) that occurred exactly once, and it was counted exactly once. Line 2 means that there were 2 unique kmers (AT and AA) that each occurred 3 times, for a total of 6 occurrences.

    Therefore - if you want to plot the coverage with respect to the genome, I suggest plotting the "unique" column. And to clarify, the number of "unique kmers" is not the same as the number of kmers that only occur once (I would call those "singleton kmers") - the second number of row 1 gives you the number of singleton kmers counted (1, in this case).
    Last edited by Brian Bushnell; 08-29-2014, 12:52 PM.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Latest Developments in Precision Medicine
      by seqadmin



      Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

      Somatic Genomics
      “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
      05-24-2024, 01:16 PM
    • seqadmin
      Recent Advances in Sequencing Analysis Tools
      by seqadmin


      The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
      05-06-2024, 07:48 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 05-24-2024, 07:15 AM
    0 responses
    147 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    160 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    162 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-22-2024, 02:06 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Working...
    X