Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • AdrianP
    Senior Member
    • Apr 2011
    • 130

    bwa map single and PE reads to ref?

    Hello,

    I want to store detect my variants in a VCF format. For that I need to map my PE reads (100x2) to reference. What I have discovered however is that for a lot of my PE reads, the fragments size is smaller than 200bp, which means some PE reads overlap, increasing the coverage of a region artificially.

    I thought I would merge the PE reads with SeqPrep to place all PE reads that overlap in a merged.fastq file.

    My question is, how do I then map both unmerged PE reads and merged SE reads to the genome with bwa? I only know how to do it if it's only SE or only PE.

    Also, does this approach sound reasonable?

    Adrian

    Biostar: http://www.biostars.org/p/97423/#97430
  • Brian Bushnell
    Super Moderator
    • Jan 2014
    • 2709

    #2
    Map the single-ended reads, then map the paired reads, then merge the two sam files. We do that all the time.

    Comment

    • AdrianP
      Senior Member
      • Apr 2011
      • 130

      #3
      Sorry I have never merged 2 sam files together, how would I do that?
      Code:
      cat *.sam > new.sam
      ?

      Thanks for the advice!

      Comment

      • Brian Bushnell
        Super Moderator
        • Jan 2014
        • 2709

        #4
        Try samtools merge.

        Comment

        • dpryan
          Devon Ryan
          • Jul 2011
          • 3478

          #5
          As I mentioned on Biostars, just use a variant caller that isn't confused by paired-end reads. GATK is one such example.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Pathogen Surveillance with Advanced Genomic Tools
            by seqadmin




            The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
            03-24-2025, 11:48 AM
          • seqadmin
            New Genomics Tools and Methods Shared at AGBT 2025
            by seqadmin


            This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

            The Headliner
            The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
            03-03-2025, 01:39 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 10:17 AM
          0 responses
          7 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-20-2025, 05:03 AM
          0 responses
          49 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-19-2025, 07:27 AM
          0 responses
          59 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-18-2025, 12:50 PM
          0 responses
          50 views
          0 reactions
          Last Post seqadmin  
          Working...