Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • weird kmer content in illumina PE reads

    Hello

    My name is Gabriel. I'm writing here because I'm analyzing Illumina reads (generated in a Hiseq 2000) from a genome of a particular insect species. So far, I've managed to remove the adapter sequence (including the indexed adapter), but when checking my filtered FastQ files with the latest FastQC version (V 0.11.2) I am seeing a weird kmer pattern in the 5' region, it seems that a particular sequence is over represented, but the overrepresented sequence module does not show anything weird.

    Also, the Kmer content overrepresented has a strong bias towards GC (i.e GGCCCGG, GCCCGGG and so on). I've also managed to overlap the Kmers to this sequence GGGCCATACTAGTACTGGATGCATCTGCAGGATATCGCGGCCGC but so far I've not been able to find anything related to this particular sequence. I'm concerned wheter it is OK to just trim this sequence, as I don't know how which meaning has this particular pattern.

    So far and during my web search, I've only seen similar patterns when analyzing RNA-seq data, but this is not the case. Also, the "bad sequence" example from FastQC webpage shows a similar pattern, but in the 3' end, not in the 5' region, as this is my scenario.

    It is worth noting that I have Paired end (2x100) files, and both files (1 and 2) have the same pattern.

    I have attached the Kmer module graphs, I can add more information if needed.

    Thank you very much, (and sorry for my english :P)

    Gabriel
    Attached Files

  • #2
    Hello gab0!

    I am facing the same problem as you and I would like to know whether you found out where the sequence GGGCCATACTAGTACTGGATGCATCTGCAGGATATCGCGGCCGC comes from?

    Thank you!

    Comment


    • #3
      Hello Svitlana
      I looked at this sequence from your other post http://seqanswers.com/forums/showthread.php?t=78247 and the reverse complement matches TruSeq Process controls CTA-150bp, CTA-450bp, CTA-550bp, and CTA-850bp.
      Josh Kinman

      Comment


      • #4
        Originally posted by jdk787 View Post
        Hello Svitlana
        I looked at this sequence from your other post http://seqanswers.com/forums/showthread.php?t=78247 and the reverse complement matches TruSeq Process controls CTA-150bp, CTA-450bp, CTA-550bp, and CTA-850bp.
        You are right jdk787, sorry I didn't see your first response. Thank you again!

        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
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X