Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Weird FastQC reports on NextSeq 500 data

    Greetings,

    We recently obtained some NextSeq500 data and I've been tasked with processing it. We were provided with deconvoluted FastQ files. I ran those via FastQC (FastQC-0.11.3) and got some strange results on the 1) per base sequence quality and 2) per tile sequence quality (See attached). I've also attached the full FastQC report as a PDF.

    Any thoughts - I don't know what to make out of these. Thanks,

    J
    Attached Files

  • #2
    There is nothing weird about these results. Looks like you have excellent sequence quality and there are no problems with any tiles. You appear to have a little adapter contamination but a pass through a trimming program (bbduk.sh, trimmomatic, cutadapt) can take care of that.

    Comment


    • #3
      Base qualities look poor towards the 3' end

      Hi,
      I have much more weird looking plots for adapter content and for the base quality distribution


      According to this fastqc result, looks like about 35% reads contain illumina universal adapters. Tried to run it through cutadapt. This flagged >45% adapters present.

      Total read pairs processed: 4,605,709
      Read 1 with adapter: 2,226,093 (48.3%)
      Read 2 with adapter: 2,177,668 (47.3%)
      Attached Files

      Comment


      • #4
        The quality, particularly for read #2 in a pair, typically decreases a bit with length, that's expected. Adapter contamination will happen whenever you read length is longer than the fragment you sequenced. When it's on the 3' end like that then that's what's happening. Just trim you data, as you should be doing anyway, and the results will be fine.

        These plots aren't "weird", they're pretty much what I see all the time for many types of experiments. Don't worry too much when FastQC tells you a test fails, those aren't even applicable to many types of sequencing experiments.

        Comment


        • #5
          Thanks dpryan

          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
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          9 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