Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Help for Fastx_clipper

    I am a newbie to this forum. I currently use FastQC and fastx for my RNA-seq data cleaning (75bp paired end).

    From FastQC, I got some over-represented sequence (0.1-1% OPS). Some of them are annotated as Truseq adapters or PCR primers, so I treat them as adapter and try to remove them from my raw dataset. When I use fastx_clipper -a OPS, it seems trimmed more then I expected. So does it mean it allow mismatch or some sequence contain part of the OPS are also get trimmed, and leaves me a lot of short reads and FastQC reports become worse. Anyone have similar experience and could you share with me the cretiera you used for this clipper command?

    By the way, anyone know where to find the fastx source code? It seems not on the website.

    Thanks very much for your time and effort!

  • #2
    Hi, have a look at this thread: http://seqanswers.com/forums/showthread.php?t=16056

    Might be that fastx_clipper doesn't always do what you expect; you might have to validate the output or to use cutadapt instead.

    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
    12 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
    52 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