Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • reference sequence coverage please

    Hi all,

    How to calculate how much percentage of reference sequence is covered/not covered (because of gaps) after alignment?

    Thanks,
    Last edited by sbsusers; 09-05-2012, 06:57 AM.

  • #2
    1) figure out size of reference (should be about 3.1 GB for h. sapiens).

    2) Figure out what's covered. Look at samtools depth command. Examine the output. Example is this :
    chr2 89197150 13
    chr2 89197151 13
    chr2 89197152 13
    chr2 89197153 13
    chr2 89197154 7

    note that there's coverage for many locations but sometimes it's zero so we can't just count the number of lines outputted so we have to do something like this ...

    samtools depth yourfile.bam | awk '{if ($3>0) print $0}' | wc

    3) Do a little algebra using answers from #1 and #2.

    Comment

    Latest Articles

    Collapse

    • 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
    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin




      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
      04-22-2024, 07:01 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 05-14-2024, 07:03 AM
    0 responses
    19 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-10-2024, 06:35 AM
    0 responses
    44 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-09-2024, 02:46 PM
    0 responses
    54 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-07-2024, 06:57 AM
    0 responses
    42 views
    0 likes
    Last Post seqadmin  
    Working...
    X