Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • A question about alignment depth

    What is the definition of 'alignment depth', it seems it is also called 'reads depth'? what information can be acquired from 'alignment depth'?

    Thanks.

  • #2
    Essentially, it boils down to how many times each sequenced base is covered. The more depth, the more confidence you gain in your data.

    At the most basic level, most organisms I've worked with are diploid, so you get information about the SNPs present in the alleles (eg, homozygous or heterozygous.) I've seen various presentations where people have claimed that upwards of 50x coverage is required to truly required to really know if you have heterozygous SNPs, though what the minimum dept required really is depends on the technology and the method used to call SNPs.

    There are always inherent errors in the wet lab as well as the dry lab portions of any experiment. The more depth you get, the more support you get for your observations.

    Does that help?
    Last edited by apfejes; 01-14-2009, 09:04 AM. Reason: typo & clarity
    The more you know, the more you know you don't know. —Aristotle

    Comment


    • #3
      So helpful.
      Thanks million.

      Comment


      • #4
        What is the difference between depth and coverage?
        When someone says that obtained 50X average coverage for a specific window, does this mean the depth?

        Comment


        • #5
          Strictly speaking, I think they're exactly the same, but people often use them in different contexts, particularly with haploid/diploid organisms.

          When talking about a window, you can probably use them interchangeably.

          When talking about sequencing a SNP in a diploid organism, it's possible that you observe the SNP on one one half of the reads that map to a given point in the reference genome. Thus, you might have a depth of 50 at that point (50 reads cover that location), but the SNP itself has a coverage of 25X. (only half of the reads at that location have the SNP.)

          I'm sure there are people who will use them in the opposite manner as well.
          The more you know, the more you know you don't know. —Aristotle

          Comment


          • #6
            Ok, thank you for the reply! It makes sense

            Comment

            Latest Articles

            Collapse

            • 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 on Modified Bases...
              Yesterday, 07:01 AM
            • seqadmin
              Current Approaches to Protein Sequencing
              by seqadmin


              Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
              04-04-2024, 04:25 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 04-11-2024, 12:08 PM
            0 responses
            51 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 10:19 PM
            0 responses
            50 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-10-2024, 09:21 AM
            0 responses
            44 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 04-04-2024, 09:00 AM
            0 responses
            55 views
            0 likes
            Last Post seqadmin  
            Working...
            X