Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • thiNGS
    Member
    • Sep 2014
    • 24
    #1

    mark and remove duplicates

    Hi everyone! if I mark duplicates in my BAM file using samblaster can I remove them using samtools rmdup?
    I was wondering if samtools consider the duplicates flagged by the other tool and just remove them or if it marks again the duplicates itself.
    Tags: None
    • dpryan
      Devon Ryan
      • Jul 2011
      • 3478
      #2
      Samtools rmdup doesn't look at the dup flag that is presumably set by samblaster. Instead, just use
      Code:
      samtools view -bF 0x400 original.bam > dedup.bam

        Comment

        Previous template Next

        Latest Articles

        Collapse
        • kinpict.com
          Reply to 16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
          by kinpict.com
          The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.
          Today, 06:37 PM
        • 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,...
          10-30-2026, 06:46 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Gene Copies Once Dismissed as Junk DNA Shape Animal Adaptation and Human Disease by SEQadmin2
        Started by SEQadmin2, 11-12-2026, 07:59 AM
        0 responses
        26 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        11-12-2026, 07:59 AM  
        WashU Medicine Study Verifies Methods for Tracking Genetic Mosaicism by SEQadmin2
        Started by SEQadmin2, 11-05-2026, 09:25 AM
        0 responses
        35 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        11-05-2026, 09:25 AM  
        HuBMAP Portal Offers Free Access to Single-Cell Data from Healthy Human Tissues by SEQadmin2
        Started by SEQadmin2, 11-03-2026, 11:54 AM
        2 responses
        55 views
        0 reactions
        		 Last Post kinpict.com
        by kinpict.com
        Today, 06:49 PM  
        Genome Sequencing Reveals Large, Repeat-Rich DNA in Trapdoor Spider Named for Stephen Colbert by SEQadmin2
        Started by SEQadmin2, 10-28-2026, 09:57 AM
        0 responses
        175 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-28-2026, 09:57 AM  
        View All
        Working...