Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How can I see the assembly sequences in cufflinks output ?

    Hi,everyone.

    I want to use RNA-seq data to find NATs,so i use tophat and cufflinks to map and assemble reads.

    my question: Does cufflinks output can see the assembled sequences??

    I only can see the exons start and end.

    How can I get the assembled sequences?? Thanks.

    Eric

  • #2
    Cufflinks doesn't "assemble" the reads it merely annotates and quantifies the number of reads that map to each separate location of the genome e.g. an exon.
    To view how the reads have mapped try IGV (http://www.broadinstitute.org/igv/)
    which takes an indexed .BAM file from tophat

    Hope this helps

    Comment


    • #3
      try gffread

      Comment


      • #4
        Tophat unmapped Bam

        For tophat unmapped bam. I want to trim reads at 50bp. Anyone knows how to do this trim. Thank you!

        Comment


        • #5
          just i think

          Originally posted by liweixie View Post
          For tophat unmapped bam. I want to trim reads at 50bp. Anyone knows how to do this trim. Thank you!
          是不是要编程删除50bp下的片段。我理解正确吗?
          I think it should be done by writting a program of perl/c/c++, you can trim the sequence <50. Does it right?

          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
          7 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          7 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
          66 views
          0 likes
          Last Post seqadmin  
          Working...
          X