Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • trimming reads in tophat

    Our short Illumina reads appear to have varying lengths of adapter oligo at the 3' end.

    Using bowtie I can use either '-l 20' to set the seedlength or '-trim3 16' to ignore 16 bases at the 3' end when doing alignments. There doesn't appear to be any way to do with same thing with tophat.

    How do people handle this when running tophat? Should I just truncate all the reads to 20 bases before passing them to tophat?

    Thanks in advance.

  • #2
    cutadapt may help

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Recent Innovations in Spatial Biology
      by seqadmin


      Spatial biology is an exciting field that encompasses a wide range of techniques and technologies aimed at mapping the organization and interactions of various biomolecules in their native environments. As this area of research progresses, new tools and methodologies are being introduced, accompanied by efforts to establish benchmarking standards and drive technological innovation.

      3D Genomics
      While spatial biology often involves studying proteins and RNAs in their...
      01-01-2025, 07:30 PM
    • seqadmin
      Advancing Precision Medicine for Rare Diseases in Children
      by seqadmin




      Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...
      12-16-2024, 07:57 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 03:17 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 01-03-2025, 11:18 AM
    1 response
    36 views
    1 like
    Last Post Tonia
    by Tonia
     
    Started by seqadmin, 12-30-2024, 01:35 PM
    0 responses
    40 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 12-17-2024, 10:28 AM
    0 responses
    45 views
    0 likes
    Last Post seqadmin  
    Working...