Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Using TopHat2 RNA-Seq Data IOn-Torrent

    Hi everyboy. I have a quick question about the "--library-type" option in the Tophat2. If the reads are from single end, RNA-seq (poly(A)) LIbrary using kit Ion Total RNA-Seq Kit v2 which options is correct. FR Unstranded? the another are -FR- First strand or FR-Second Strand. Can Anyone clarify me this?

    Thanks in advance
    Regards

  • #2
    From the manual for the kit, The Ion Adaptor Mix v2 constrains the
    orientation of the RNA in the ligation reaction such that hybridization with the Ion
    Adaptor Mix v2 yields template for sequencing from the 5′ end of the sense strand.

    So you'd want to use the fr-secondstrand option for mapping

    Comment


    • #3
      thanks so much

      Comment


      • #4
        I found this post helpful: http://onetipperday.blogspot.co.uk/2...pe-to-use.html

        Essentially I chose a few reads, BLAT to a genome and infer the library-type from the mapping result.
        Last edited by mlou; 12-09-2014, 01:07 PM.

        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
        49 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