Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Control Lane - PhiX

    Hi,

    We have been sincerely using the control lane in all our solexa runs thus far. The auto5 option for Solexa pipeline phasing, when control is in lane5, uses the control lane data to generate matrix and phasing on all other lanes.

    I am curious as to what if we skip the control lane. The matrices anyways look pretty similar, and the slight changes we see in the control matrix as well, is ignored by the solexa rep

    Anyone here tried looking into this? Any other alternatives to skip the control lane and still get some QC, meanwhile, taking advantage of one extra lane of another sample.

    thanks..
    --
    bioinfosm

  • #2
    There's a few threads discussing the options for omitting the control lane. People from the Broad spike their samples with a mixture of DNA samples that, at each base position, read equally A, G, C and T. Other people don't use it at all if they're confident of the sample they're running. Illumina doesn't support any option other than the PhiX control lane, of course.

    Comment


    • #3
      Thanks Scott, but I am not sure what threads you refer to.

      It is the option of 'not using the control lane at all, if confident of the sample' ... how do people prefer doing that, etc.
      --
      bioinfosm

      Comment


      • #4
        Oh, actually on looking around a bit more, I think I've gotten confused as to the source of the information to which I was referring. It was posted on the Solexa google group...



        I have heard a few people mention that if they are re-sequencing, and they know the base composition of their sample, then the phiX lane isn't really required if the base composition around 50% GC.

        Disclaimer: I'm just relaying what I've heard, and what I've seen written... I haven't tried any of the 'no PhiX control' methods!

        Cheers,

        Scott.

        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
        7 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        7 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
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X