Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • UniFrac analysis for Sanger and 454 pyroseq data

    Hi, all!
    I have a dataset from Sanger (12 seqs ~350-500bp) and 454 sequencing (32000 seqs (140 OTUs) ~500bp).

    And here is a question:
    It's possible to compare OTUs seqs from 454 with Sanger by weighted\unweighted UniFrac analysis?

    And one more question: It's correctly to do this if I have so different size of datasets - 12 seqs vs. 140 OTUs? Could I say that my 12 Sanger seqs are equivalent to OTUs in metagenome?

    Thanks,
    Kind regards!

  • #2
    Could I say that my 12 Sanger seqs are equivalent to OTUs in metagenome?
    I'd be hesitant in saying so. Different platforms employ different strategies to generate data. Even if you'd sent same samples in pyro and sanger machines it's possible to not have same thing sequenced equally.
    Bioinformaticscally calm

    Comment


    • #3
      Thanks for your answer, bio_informatics!

      Could you advise me something in this case? May be there is any way to compare my datasets?

      Comment


      • #4
        Originally posted by odyssey View Post
        Thanks for your answer, bio_informatics!

        Could you advise me something in this case? May be there is any way to compare my datasets?
        1- I'd take FASTA file before chimera checks from both the runs, merge, remove chimeras and proceed for classification.

        2- Maybe reaching out to QIIME folks on their forum would be fruitful.
        Bioinformaticscally calm

        Comment


        • #5
          Ok, thanks a lot for your advice

          Comment


          • #6
            Originally posted by odyssey View Post
            Hi, all!
            It's possible to compare OTUs seqs from 454 with Sanger by weighted\unweighted UniFrac analysis?
            I've not done Unifrac analyses but one issue while merging OTUs from different runs is that there can be duplicate OTUs.
            That's why I suggested to merge FASTA from both runs, then cluster, remove chimera (or remove chimera then cluster).
            I hope this makes sense. Sorry, for not clarifying earlier.
            Good luck.
            Bioinformaticscally calm

            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