Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Sample sequencing performence depending on index?

    Hi,
    I have some Illumina exome data from different runs on NextSeq. I see quite some difference in the number of produced reads per sample, which seems to correlate with the used index.
    It occured using different batches of chemicals and I ruled out positional effects in wet lab.

    Has anyone run into this problem before?

  • #2
    Were the libraries made at different time points or at the same time? By the same person using the same protocol?

    Comment


    • #3
      Hi GenoMax,
      different time point, different persons, same protocol.

      Comment


      • #4
        Then you can't really say for sure that the index is the culprit (perhaps you put that reason down since you can see it is the results). It could be related to library made by a different person and/or other factors.

        Comment


        • #5
          Sry. I should have answerd more precise.
          For each single run all libraries were prepared just before the run was started by just one person. The person producing the library was different for different runs, but not for all.
          So there is no connection between MID and Person or MID and timepoint which could explain the effect.

          From your answers I conclude that you have never seen such an effect

          Comment


          • #6
            If different captures with the same index tend to have lower reads than others it could be due to multiple G residues in index sequence which would affect quality of index read and result in read loss during demultiplexing.

            Comment


            • #7
              If @nucacidhunter is right then these libraries if run on a 4-color sequencer will look equivalent. Something you will have to test.

              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