Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Comparison of two sets of miRNAs

    Hi all,

    i have two sets A and B of miRNAs. How i can make a comparison of them considering common elements and not ?

    Is there any tool that makes this type of comparison ?

    Thanks in advance for your help

  • #2
    which type of data ? explain a little bit more about your problem

    Comment


    • #3
      There are two sets of miRNAs one coming out from a leaf and the other from the flower of the same Orchid. I have to know what are the differences between these two sets:
      Elements in common and not. They are both in fasta format and in replicate (trimmed, filtered and collapsed with galaxy tools) originally coming out from a 454 platform.

      they apper like this:

      >1-8490
      ACGTCACTCTCTCC..
      >2-7990
      CGTCAATCGCCTCC..
      >3-6696
      ACGTGCACTGCATG..

      the first number is the Id , the second represents the number of occurences.

      I need to evidence what are the differences fromt he two sets. Do you have any advice ??

      tnx

      Comment


      • #4
        Ok


        First annotate your reads : align them against mirbase databse (with blats per example) and then count for each miR, the number of reads.

        After that in R create a matrix : each line represent one miR, each column a sample. Then use DESeq or edgeR for the DE analysis

        Comment


        • #5
          thank you very much for your fast reply. Is a problem that most of the miRNAs are novel and have no match with the database ??

          Comment


          • #6
            maybe try miRDeep before DE analysis

            Comment


            • #7
              Yes, i'v just done it with mirDeep but being this type of Orhichid not yet annotated i have a lot of no matching elements

              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