Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Differentiate DNA-Seq / RNA-Seq and Exome sequencing data

    Hi there,

    If you have situation that you have files from three sequencing platforms ( DNA-Seq / RNA-Seq and exome sequencing ) and do not know which belongs to which, can you distinguish them in some way?

    I have an idea, but wanted to check what you guys think?

    - Map some reads from each technology to one chromosome ( to save time and computing power )

    - The reads that map everywhere, exons + introns = DNA-Seq reads

    - Reads that map to exons +- 50bp = Exome seq reads

    - Reads which have very less or zero coverage in intronic regions = RNA-Seq reads.

    What do you guys think? Is there any other way? ( Other than files sizes )

    Thanks a ton,

  • #2
    Seems reasonable. If you have a known chromosome. :-)

    Comment


    • #3
      Originally posted by westerman View Post
      Seems reasonable. If you have a known chromosome. :-)
      What do you mean by a known chromosome?

      Comment


      • #4
        Try working with, oh, say data from a Whale. :-)

        In some ways, if you are making the thought experiment of "how do I differentiate between different unlabeled data sets" then you might as well make it even more interesting -- try to differentiate between data that is both unlabeled in platform and species.

        Given data from a human sample, then, yes your approach seems reasonable.

        Comment


        • #5
          How about if we make bed files for the alignments of exome and whole genome?

          Would we be able to differentiate them using the UCSC browser ? I believe the tracks for the two should look very different.

          What do you guys think ?

          Comment


          • #6
            You could better differentiate between Exome and RNA-seq reads by watching the mean insert size, since aligning RNA-seq reads that span exons would lead to long insert sizes and/or split-reads. If the RNA-seq data is stranded than it's even easier.

            I guess the easiest method for visualization is IGV (http://www.broadinstitute.org/igv/)

            So take a subset from those reads, align them and watch them in IGV. (the only problem you might run into is a very shallow coverage which doesn't give you a nice picture in every gene...)

            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