Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Mapping strand-specific data with TopHat

    I have RNA-seq data that I want to map using TopHat. The library prep was done using ScriptSeq v2, and the sequencing using Illumina.

    The R1 sequences the sense cDNA from start to finish. The R2 sequences the antisense cDNA from finish to start.

    The --library-type option fr-unstranded says that "Reads from the left-most end of the fragment (in transcript coordinates) map to the transcript strand, and the right-most end maps to the opposite strand.", which would seem to be just what I need.

    However how does it deal with sense cDNA that has been expressed from the negative strand of the DNA? If an R1 read is just that, then wouldn't the read have to be reversed to map to the genome?

    Has anyone dealt with anything similar, and if so, do you know which settings I should use for TopHat?

  • #2
    I have the same problem.
    I prepared my library with Scriptseq V2 (directional).

    The sequencing was done with Illumina PE 2*76bp.


    Can anyone explain more precisely the --library-type option of TopHat ?
    I don't understand the difference between "fr-unstranded" and "fr-secondstrand"


    What's the best parameters in my case ?

    Thank-you.
    Last edited by Oliviervg; 03-13-2012, 08:00 AM.

    Comment


    • #3
      Any help would be very appreciated !
      Thank you !

      Comment


      • #4
        TopHat doesn't have those options, are you sure you're not thinking of Cufflinks?
        For the scriptseq v2 kit I would use the fr-secondstrand librarytype since the first read will be the left-most in transcript coordinates.

        Comment


        • #5
          Thank you for your answer, I m going to use fr-secondstrand.
          And, my TopHat 1.4 has those options !

          Comment


          • #6
            You're right, they were just well hidden (and I never had use for anything other than the default).

            Comment


            • #7
              Just a reminder, if you did not see this:

              Comment

              Latest Articles

              Collapse

              • 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
              • seqadmin
                The Impact of AI in Genomic Medicine
                by seqadmin



                Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                02-26-2024, 02:07 PM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, 03-14-2024, 06:13 AM
              0 responses
              32 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-08-2024, 08:03 AM
              0 responses
              71 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-07-2024, 08:13 AM
              0 responses
              80 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-06-2024, 09:51 AM
              0 responses
              68 views
              0 likes
              Last Post seqadmin  
              Working...
              X