Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SOLiD Barcoded Adapter Trimming

    Dear all,

    I've run a barcoded SOLiD run with a set of 12 small RNA samples. Following the sequencing run, I've performed the primary analysis and downloaded the csfasta (F35) and qual files.

    On visualising the reads, they are all 35nt as expected and I therefore need to remove adapter sequence. My question is what sequence I should be expecting...

    As I understand, the barcode is read in a separate sequencing reaction and therefore is not part of this 35 read. Also as the read is read from P1, it is not the P2 adapter as this is more than 35 away from the sequence start site.

    My only guess is that it is the barcode "adapter" which seems to be PCR'd in when using the various barcoded primers.

    Can anyone confirm whether I am correct? And if so, have the sequence of this adapter (I presume it is conservered across all the barcodes)...

    My working tell me the sequencing should be...

    CGCCTTGGCCGTACAGCAG

    however this doesn't give a good % trim (around 20 %)

    Many thanks,

    D

  • #2
    or the reverse complement

    CTGCTGTACGGCCAAGGCG

    Comment


    • #3
      Are you doing your trimming in base-space or color-space?

      Comment


      • #4
        I'm doing it in colour-space using CLC Bio...

        Comment


        • #5
          Hi DrDTonge,

          I have a similar SOLiD data of small RNA samples with every read being 35bp long. Did you find a solution to problem you posted? Is "CGCCTTGGCCGTACAGCAG" the only adapter that you trimmed?

          Thanks

          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
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          51 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          68 views
          0 likes
          Last Post seqadmin  
          Working...
          X