Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • PFS
    Member
    • Mar 2010
    • 55

    #1

    Find mates in a SAM file

    I want to identify the actual pairs of reads in a SAM file that potentially has multiple alignments for the same given pair.

    Is it sufficient to check whether two lines in the SAM file have same QNAME?

    Do I have to check for POS (start) and PNEXT (start of mate) fields and make sure they are matching between two lines?

    I am aware of the meaning of SAM flags to identify paired and mapped reads. Simply checking the flag, however, does not allow me to identify the actual pair.

    Thanks in advance.
  • lindenb
    Senior Member
    • Apr 2010
    • 143

    #2
    cross-posted: https://www.biostars.org/p/149205/

    Comment

    Latest Articles

    Collapse

    • SEQadmin2
      16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
      by SEQadmin2




      NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
      10-30-2026, 06:46 AM
    • SEQadmin2
      Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
      by SEQadmin2



      Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

      Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating
      ...
      10-14-2026, 09:55 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by SEQadmin2, 10-28-2026, 09:57 AM
    0 responses
    45 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 10-28-2026, 09:51 AM
    0 responses
    26 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 10-22-2026, 11:13 AM
    0 responses
    75 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 10-22-2026, 10:48 AM
    0 responses
    49 views
    0 reactions
    Last Post SEQadmin2  
    Working...