Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • FastQC: odd kmer content

    Hi,
    I'm checking the data quality using fastqc for the Illumina Hi-Seq2000 reads and got odd kmer patterns (see attachment). Although an old thread suggested that 5' pattern is common, I want to know how to eliminate the odd patterns for GGGGG, AAAAA and TCTTC. Could you please help to interpret and get rid of them?
    Thanks in advance!
    Attached Files

  • #2
    TRIMMOMATIC, or any other read cleaning program, should clean those up. I would use options: SLIDINGWINDOW:4:15 HEADCROP:15 MINLEN:36
    Then run FastQC again and you should see a much nicer report, if you are just mapping to a reference genome then cleaning reads is less of an issue so you could leave out the HEADCROP (which cuts bases from the start). But if you are assembling de-novo then I would cut that non-random sequence at the start.

    Comment


    • #3
      Thanks for your help!
      I intend to calculate genes/transcripts expression levels. Do I have to cut the 5' 10 bp?
      I'm wondering what causes the patterns of for GGGGG, AAAAA and TCTTC, because I saw those patterns in other tens of RNA-seq data files.

      Comment


      • #4
        Like I said, you only need to cut if doing a de-novo assembly because the non-randomness of the start of the reads could cause problems in assembly, if just aligning to a genome then the read should align anyway. The non-randomness of the start is usually caused by the 'random' primers used to make cDNA. The stretch of Gs or As are either bad quality reads or legitimate stretches of repeats that happened to get sequenced, either way the SLIDINGWINDOW option seems to remove them.

        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
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        8 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
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X