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  • How can I remove DNA from RNA dataset by bioinformatics?

    Dear all,

    I am a new starter as I just start to do research related to bioinformatics.
    And I am now facing a big problem.

    My demonstrator told me that my RNA data contain DNA by blasting the whole dataset. And now he would like me to find out a tool to remove DNA data.

    my research is related to metagenomics research, using RNA but not DNA.
    As I have no reference to filter DNA that may come from difference species, could anyone give me a hand?

    Is there any tools to remove DNA from RNA data that with higher accuracy than removal of blast result which indicate DNA features ?

  • #2
    Silly answer: Throw away any sequences that don't have a "U" in them :-)

    Proper answer: Are the RNA and DNA from the same organism?

    Comment


    • #3
      for the proper answer:
      NO, DNA and RNA come from different organism.

      Since my research relate to metagenomics

      Comment


      • #4
        Originally posted by hellsingwyk View Post
        My demonstrator told me that my RNA data contain DNA by blasting the whole dataset. And now he would like me to find out a tool to remove DNA data.

        my research is related to metagenomics research, using RNA but not DNA.
        As I have no reference to filter DNA that may come from difference species, could anyone give me a hand?
        Those two sentences do not hang together. How can you know that you have DNA in your RNA via Blast yet not know the DNA reference?

        In any case take the Blast results and use that information (i.e., the matching sequences) to filter the RNA.

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        • #5
          And perhaps you could try starting only one forum thread instead of two. That way you may get answers that build on each other instead of having to answer the same question over again.

          Comment


          • #6
            I am really sorry..............
            Since this is my first time to join in this forum. Next time I will not ask same question in two different forum threat.

            As I only need those RNA data, and my demonstrator told me that he found DNA contamination inside the dataset using blast. Therefore, I would like to ask if there is careless mistake in sample preparation for DNA removel, can we remove DNA from the dataset by bioinformatics when I am doing metagenomics research with no references?

            Comment


            • #7
              Originally posted by hellsingwyk View Post
              As I only need those RNA data, and my demonstrator told me that he found DNA contamination inside the dataset using blast. Therefore, I would like to ask if there is careless mistake in sample preparation for DNA removel, can we remove DNA from the dataset by bioinformatics when I am doing metagenomics research with no references?
              Are you just looking at 16S rRNAs or transcripts in general? If the former, then blasting could be useful (though perhaps those better versed would disagree), though I could think of more efficient ways to go about things. If not, without knowing the likely sources of the contamination and having a reference sequence for them (not to mention that the sources of contamination would have to have a significant enough genetic difference from your sources of interest to allow reliable discrimination), there is no way to do that.

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              • #8
                may be start all over using a good DNAseI??

                Comment


                • #9
                  this is a good idea..........

                  Comment

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