Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • miRNA analysis

    Hi all,

    I am trying to work on a small RNA dataset generated using Illumina TruSeq™ Small RNA protocol.

    I have run the data through the various tools specialised for miRNA analysis (such as miRDEEP, miRAnalyser for miRNA identification and novel miRNA prediction),

    In addition to many reads hitting known mouse miRNAs, other ncRNAs and possible candidate miRNAs...

    *****
    I also ended up getting many reads (a big percentage) which align with the mouse genome :Both transcribed regions and unannotated regions.


    My first question is :
    Why should my reads have perfect (no bp mis-alignment) hits against mRNAs? Would these represent by-products of genes degradation (with the gene fragments in the acceptable length range around 25 nt) )? Any suggestions?

    These hits are present through out the genome and show similar presence (in terms of read coverage and read numbers) in most (if not all) places of the genome. So when I map the reads using bowtie against the genome ..I see a very similar pattern in both samples.

    Should I even consider checking a possible differential gradient for these reads between the two samples?

    Secondly:
    What are these reads hitting in big numbers against unannotated (mostly intronic regions!!) of the genome?

    Any ideas are welcome.

    cheers,

    Nandan

  • #2
    A couple of questions:

    1. what sort of mRNAs are they aligning too? (randoms, or a particular kind?)

    2. i have read about miRNAs coming from introns, called miRTrons. Did you check about this?

    3. any thoughts about sample contamination or sample prep issues?

    edit: I guess the other question is, are the mRNA-hits targets of these miRNAs (even though you might expect some bp mismatches)
    Last edited by Kennels; 07-07-2011, 04:02 PM.

    Comment


    • #3
      Why should my reads have perfect (no bp mis-alignment) hits against mRNAs?
      Some mature miRNA from duifferent species, miRNA from the same miRNA family or isomiR from the same hairpin have only 1-2 nt difference. So most packages only allow perfect match.

      Comment


      • #4
        Originally posted by petang View Post
        Why should my reads have perfect (no bp mis-alignment) hits against mRNAs?
        Some mature miRNA from duifferent species, miRNA from the same miRNA family or isomiR from the same hairpin have only 1-2 nt difference. So most packages only allow perfect match.
        Perfect matches against mRNAs are perfectly normal. They are degradation of mRNAs.

        Did you used ncRNA databases ( RFam ) to annotate reads that aren't miRNAs ?

        For the introns alignment, like Kennels said, maybe mirtrons ?

        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