Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Library size selection for bacterial RNAseq

    Hello,
    I've been reading the forum and am confused about what size of library to select for RNAseq. We want to capture small RNAs (and all mRNA) but don't want to select too short of fragments as to miss the rest of the transcriptome information and/or have excessive sequencing into the adapter region.
    The sequencing provider we've been talking to recommends Illumina 75 bp paired-end reads for RNAseq. From this, I assume that a library size of 200 bp - 400 bp would be optimal. This would mean a fragment size of ~70 bp - 270bp.
    Does this sound ok?
    Any advice would be helpful.

  • #2
    Hi whitestein,
    Various issues at play here. But I would say the only major issue with your plan would be that the shorter (70 bp) fragments will probably amplify preferentially during enrichment PCR.
    Is this a de novo transcriptome or do you have reference to map to?
    --
    Phillip

    Comment


    • #3
      Thanks for the reply Philip.
      Yes, we have a reference genome to compare to.

      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
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 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