Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • RTA - bug - other options

    Hi, it appears that there is a bug in the RTA software (we are running RTA1.18.54). We are running some 16S on the MiSeq and the % > Q30 charts, we often see a sharp drop off right at the beginning of the read. Illumina techsupport have indicated that this is due to the RTA software, where it could not adjust the signal from the ATGC. RTA is involved in the primary analysis and appears crucial for generating the BCL files, does anyone know if it is possible to sidestep RTA or any other ways to compensate for this issue?
    thanks.
    Last edited by Elsie; 06-03-2014, 03:06 PM. Reason: wrong version listed

  • #2
    A further reply from Illumina:

    "Why do we see a drop in Q scores in the initial cycles of read 1? This is characteristic of runs which use our suggested V3/V4 target primers, and appears to be linked to a specific motif, though we don’t quite understand the mechanism by which signal to noise is so reduced in these initial cycles. We considered revising the design before releasing the demonstrated protocol but what we found is that this didn’t significantly impact the pass filter rates or data quality, and since it happens in the primer sequence its not affecting the part of the read used in the analysis. This means that although it looks alarming, the functional impact is essentially nil. Customers running this assay will see a very different run profile in SAV as they are accustomed to just because it is a single amplicon low diversity run."

    So maybe no need to bypass RTA but something to be aware of.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Genetic Variation in Immunogenetics and Antibody Diversity
      by seqadmin



      The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
      11-06-2024, 07:24 PM
    • seqadmin
      Choosing Between NGS and qPCR
      by seqadmin



      Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
      10-18-2024, 07:11 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 11-08-2024, 11:09 AM
    0 responses
    165 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 11-08-2024, 06:13 AM
    0 responses
    127 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 11-01-2024, 06:09 AM
    0 responses
    77 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-30-2024, 05:31 AM
    0 responses
    26 views
    0 likes
    Last Post seqadmin  
    Working...
    X