Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Time required to complete a transcriptom to Genome mapping project

    Hello All,
    I'm a new comer to NGS. However, I have years of experience in other field of Bioinformatics and I'm well
    versed in scripting/programming. Besides, I've experience in general sequence analysis.
    I wish to align raw squence reads of a transcriptome to a already sequence genome of the same organism to look for
    novel transcripts.
    I plan to use TOPHAT. I've access to high performance Linux Cluster at my University. Being a novice I think I'll need some time to learn
    about these tools, stumble on some steps and retry things.

    I wish to know how long it might take for me to complete such a project?

    Thanks

  • #2
    The first part won't take long, though it depends on the size of your genome and number of reads. You simply index the genome (one command), then map the reads (another command). Alternately, if you are only interested in novel transcripts, you could map to the transcriptome first, requiring high identity, then only map the remaining unmapped reads to the genome, which will greatly enrich for novel splices and leave you with less data to wade through.

    The analysis will take a lot longer; how long depends on how much you automate it and how big and well-annotated the genome is. There are some tools in the Tuxedo package designed for identifying novel transcripts but I have not found them to work well. I highly recommend IGV, though, for visualizing aligned reads to identify novel splices and transcripts. Incidentally, when mapping RNA-seq data to the genome to look for novel transcripts, I recommend BBMap over Tophat; it's faster and more sensitive.

    Comment


    • #3
      Many thanks for your answer. I'll be working with Mouse genome and a particular mouse tissue transcriptome.

      Thanks

      Comment


      • #4
        Since you already have experience with command line/programming it should not take longer then a month to complete the whole project (probably including the time you will need to spend on coming up to speed with things).

        That time estimate is for a modest number of samples (say < 100). If you are going to do thousand(s) then the one month estimate does not apply

        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