Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Gave the Wrong Indexes for WGS... but I know them!

    I recently sent off 100+ genomes to be whole genome sequenced and I sent the incorrect ones for a couple... but I have the correct ones! Is there a method which I can use them to determine my sequences

    Currently, I have three lane files with sequences but how can I determine which sequences belong to what sample. I tried using process_rad tags with my barcodes but cant retrieve my sequences... I see the tags when I use grep but is there a more efficient way of doing this???

    Thanks...

  • #2
    Sorry, I do not fully understand what type of information you have and what you are looking to retrieve.
    Do you see the index read sequences in the read headers?

    Comment


    • #3
      Sorry. Yes I see some but they contain Ns.

      I believe that the sequencing company didnt cleaned up the incorrect indexes for since they contain Ns in the index headers.


      I have sequence data for the lanes I ran. I am looking to retrieve the sequences that match my unique indexes as they pertain to specific individuals. They each have unique IDs. So I am trying to identify which sequences in each lane pertain to each sample.

      @G98558:222:XXXXXXX:6:1101:6258:1397 1:N:0:NCCCCTCG+NGATCTCG


      Sample I TATAGCAT GTAGTAT
      Sample II XXXXXXX XXXXXXX
      Sample III XXXXXXX XXXXXXX

      Comment


      • #4
        It sounds to me like the reads were demultiplexed, but you had given incorrect index sequences for a few samples, so those reads are still in the Undetermined file and you want to extract them? Is that right?

        I'd say if you can see them with grep you should just let that run and it would be faster than figuring out the optimal way to extract them. But it is curious that process_rad_tags doesn't see them. Have you configured it for dual indexes rather than inline RAD barcodes?
        Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

        Comment


        • #5
          Yes. Sorry my wording is awful.

          I can see them in the sequences, not the header... but I'm taking that with a grain of salt which is why I'm wondering if there is a way to do it differently.

          I'm not sure how to configure it for dual indexes, unless if you mean providing a file with index 1 and then index 2 which I have.

          Comment


          • #6
            It would be helpful to say exactly what libraries you made and then paste some example sequences of what you got back. Were most samples successfully demultiplexed? What do those reads look like?
            Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

            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
            50 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