Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • extra sequence following transcript in RNA-seq ?

    Hi,

    I did a dual-seq with pathogen and host. I found more nucleotides after the total mRNA transcript(as annotation) from the pathogen. For each sequence that mapped to the pathogen transcript in the fastq file, the strings of nuceotides following the end of the transcript, however are very different. This role out the possibility that the annotation sequence is not intact.

    Does anyone know whether this happens often? And why this would happen?

    Thanks a lot!

    Best,
    F

  • #2
    You can get this happening off the end of transcripts because the sequencer just sequences whatever it has available (if anything). For circularised DNA, this ends up being the index sequences that are attached to the ends of the reads. Have you done adapter clipping prior to mapping?

    Comment


    • #3
      Hi Gringer,

      Thanks for the quick reply. I got the data after they are removed off the index sequences. All the fragments that I get are of equal length. I just don't why there are still nucleotides after the end of the transcripts.

      Comment


      • #4
        Could you post a picture of your alignment.

        Comment


        • #5
          Hi,

          I grep the pathogen sequence from the fastq file.

          All the matched seuqence is 50bp.

          Before the space is the end of my pathogen transcript. Any nucleotides following it, I don't know what they are. Could this be technical noise?

          Thanks.
          F
          Attached Files

          Comment


          • #6
            Originally posted by FLYINGDOLPHIN View Post
            Could this be technical noise?
            If that's the case, then you should be able to tell by the quality scores in the FASTQ files. If it's substantially lower than the transcript sequence (e.g. 10ish), then it's probably noise due to the machine getting confused. It doesn't look like it's due to phasing alone, because then you'd expect to get more sequence that looks similar to the last few bases (e.g. the line that has '20' next to it).

            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