Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • chromosome rearrangements

    Hello there,

    I'm thinking to do some paired-end sequencing on a 454. Do you know if the software that comes with the sequencer can identify chromosome rearrangements from the paired-end sequence or do we need to use the custom program.
    Has someone done this type of work already? Any recommendations, tricks?

    Thanks for you help,

    Kiki

  • #2
    The 454 assembly software can identify the paired-end information from the reads, but what you mean chromosome rearrangements ?

    Comment


    • #3
      chromosome rearrangements

      Hello,
      By chromosome rearrangements, I mean the cases where both paired-end sequences, don't match the reference genome sequence at the same place.
      For example one paired-end sequence matches on the expected location but the other paired-end sequence matches on another chromosome and on the same chromosome but much further away than expected. In these cases, we have a translocation and an insertion, respectively.
      I talked to a 454 rep and it seems that the software doesn't do that and that we need a custom program to parse the paired-end sequencing data.
      Has someone done this type of work?

      Cheers.

      Comment


      • #4
        That‘s interesting.
        As i know,Each 454 Long Paired End Sequencing reads contains a mate paired_end information, and the distance between a mate pair is about 3kb. So you can split a paired_end read into two parts, then seach from the reference genome one by one using blast, if one of the two parts can matches the genome more than one, then probably we got a insertion. And if the two parts can match two different genome, we got a rearrangements.
        Last edited by owomo; 06-15-2008, 04:28 AM.

        Comment


        • #5
          You could use cross_match to detect the 44mer linker sequence and then use some perl to split the read into mates. Then you can use nucmer to map mates to the reference genome.

          PS: I have noted that most linker sequences in 3K-LT PE are not exactly 44mer. They are in the range from 20-80 bp

          Besides that, you will have to discard reads in which the mates (fragments before and after the linker) are shorter than a specified cutoff (I use 22bp).

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Genetic Variation in Immunogenetics and Antibody Diversity
            by seqadmin



            The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
            Yesterday, 07:24 PM
          • seqadmin
            Choosing Between NGS and qPCR
            by seqadmin



            Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
            10-18-2024, 07:11 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 11-01-2024, 06:09 AM
          0 responses
          24 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 10-30-2024, 05:31 AM
          0 responses
          21 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 10-24-2024, 06:58 AM
          0 responses
          25 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 10-23-2024, 08:43 AM
          0 responses
          56 views
          0 likes
          Last Post seqadmin  
          Working...
          X