Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • "beginner in alignment" question

    Hello,
    I am analyzing Roche 454 sequence data. The sequencing was performed not for whole genome but for the exons of (around) 100 genes. When I first started analyzing, I used the target sequence (exome of 100 genes) as my reference not the whole genome. After all, this target region is tiled and sequenced by Roche platform. But by doing so I am getting a lot of consequential SNPs, most of them are probably false positives.
    But when I perform whole genome alignment, I am getting reasonable/low number of SNPs.
    I checked some specific regions which are showing great variation at the number of SNPs. Turns out, some of the reads mapping to that region in the 1st alignment are not mapping there in whole genome alignment, but to some other region which is not in the target sequence.
    So my questions are;
    Is it general practice to do whole genome alignment in any given NGS project, or do I need more stringent alignment parameters when performing alignment over a specific region?
    By the way, I am using bwa and ssaha2 for alignment step.

    Thanks!

  • #2
    I noticed similar behavior looking at capture illumina reads. The capture is not very specific and there is always a lot of 'off-target' sequencing that occurs. In case of using a restricted reference sequence, a lot of those 'off-target' reads are forced to align to these regions, producing false variants.

    The best approach is to use the whole genome for the mapping of reads.
    --
    bioinfosm

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Latest Developments in Precision Medicine
      by seqadmin



      Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

      Somatic Genomics
      “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
      05-24-2024, 01:16 PM
    • seqadmin
      Recent Advances in Sequencing Analysis Tools
      by seqadmin


      The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
      05-06-2024, 07:48 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 01:32 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-24-2024, 07:15 AM
    0 responses
    199 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    221 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    232 views
    0 likes
    Last Post seqadmin  
    Working...
    X