Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Illumina pair end read extraction.

    Hi all,

    I am working with a data set of 161x161 pair-end sequences generated on the Illumina MiSeq. In short, my goal is to extract all pair-end reads that overlap a 500 bp window of my assembly (easy part). I want to be able to show linkages of polymorphisms within this window.

    The problem that I am having is that I also want to extract all paired reads that are associated to different polymorphisms, such as all reads that overlap positions 700, 750 and 1005 based on my MSA (hard part).

    Is there a good program that can extract reads from MSA, SAM or BAM alignments based on the qualifier of nucleotide positions? If so what are your suggestions?

    Thanks all for your time.

    JD

  • #2
    You can specify the coordinates that you like to extract from your bam with samtools view and make a smaller bam file.

    Then use something like bam2fastq to pull out the reads in that region.

    Comment


    • #3
      To my knowledge of samtools (correct me if I am wrong) that function only work when extracting a range, extract all reads from 400 to 900 nt based on a reference. This will not work for my application.

      My goal is to extract paired reads that overlap coordinates 700 and 750 and 1000, it is similar in concept but a very different output. However, if I am wrong could you please let me know and could you please explain the syntax for such a search in samtools.

      Thanks for the reply.

      Comment


      • #4
        Use the scanBam function from the R package Rsamtools. You can give it a set of ranges of width 1, using the what parameter to ScanBamParam.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        7 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        7 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X