Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts

  • Bueller_007
    started a topic Odd characters in samtools mpileup output

    Odd characters in samtools mpileup output

    I'm struggling to figure out what some of the characters in my samtools mpileup output are. Here's one of the offending bases (scaffold1:25513). There are many.

    Code:
    scaffold1       25513   G       20      <<,,,,,a,A,aa,a,AA..    #A.CCFG6G6F67E:F<6GF
    So it tells me that the read depth is 20, and this is confirmed by counting the number of characters in each of the last two columns. But I have absolutely no idea what the "<" character represents in the read_bases column (column #5).

    The only special characters I'm expecting to see are '.' and ',' (indicating forward and reverse matches) '+' and '-' (indicating indels), and '^' (followed by a symbol indicating read-mapping quality) and '$' (indicating the beginning and end of a read respectively).

    So can anyone tell me what '<' means in column 5?


    EDIT: To answer my own question somewhat, '<' and '>' indicate a "reference skip" according to the mpileup documentation. (Although they are not mentioned in the pileup format documentation, which is why I couldn't find them.) However, I have absolutely no idea what "reference skip" means, so I'm still out of luck. If it's referring to a base that is not covered (e.g. due to splicing) then shouldn't the coverage ideally be reported as 18, not 20?
    Last edited by Bueller_007; 08-26-2011, 04:52 PM.

Latest Articles

Collapse

  • SEQadmin2
    Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool
    by SEQadmin2



    CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

    Despite this, “CRISPR helped turn genome editing from a specialized technique into
    ...
    07-31-2026, 11:01 AM
  • SEQadmin2
    Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
    by SEQadmin2


    Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

    The systematic characterization of the human proteome has
    ...
    07-20-2026, 11:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, 08-13-2026, 12:22 PM
0 responses
27 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 08-11-2026, 10:35 AM
0 responses
22 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 08-06-2026, 07:41 AM
0 responses
37 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 08-03-2026, 10:13 AM
0 responses
51 views
0 reactions
Last Post SEQadmin2  
Working...