Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • High undetermined reads

    Hi everyone, I have recently sequenced 1 lane of NovaSeq X Plus 10B with a sequencing provider. The library that was sequenced is a multiplex WGS library.

    I received the result and was informed that I have high undetermined reads (approximately 56%) in my library.

    They have also sent me the possible indexes for the undetermined reads and I was unable to find any of the sequences in my index list.

    The index that I have used for the sequencing was used in the past as well and nothing of sort has happened before.

    This is the %Pass filter vs %Occupied plot. The %Pass filter is in the 40-50% range, is there something wrong about this run?

    Thank you for your kind help in advance!

    Click image for larger version

Name:	pass filter plot in SAV.png
Views:	91
Size:	70.3 KB
ID:	325664



    ​
    ​

  • #2
    The %PF is low I think, but I don't think that this plot is necessarily the most helpful in resolving your issue. I haven't sequenced on an X Plus yet, but low %PF runs on the NextSeq 2000 and NovaSeq can still have good quality reads. What was the Q30 through each read, specifically the index reads? If the index reads had low quality, it's possible you could demultiplex with a higher mismatch allowance to cut down on the undetermined.

    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,”...
      Yesterday, 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, 07:15 AM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 10:28 AM
    0 responses
    17 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-23-2024, 07:35 AM
    0 responses
    20 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-22-2024, 02:06 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Working...
    X