Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How to filter FASTQ Quality?

    FASTX can do FASTQ Quality Filter (http://hannonlab.cshl.edu/fastx_tool...mmandline.html),

    [-q N] = Minimum quality score to keep.
    [-p N] = Minimum percent of bases that must have [-q] quality.

    May do know usually how do you define the minimum quality score and minimum percent of bases?

    Thanks.

  • #2
    It seems the new fastQ files have slightly different format that fastx quality filter tool cannot recognize it. Is there anything else out there?
    Thanks

    Comment


    • #3
      Originally posted by fznajar View Post
      It seems the new fastQ files have slightly different format that fastx quality filter tool cannot recognize it. Is there anything else out there?
      Thanks
      "New"? Since the FastQ format is not embedded in stone then I suppose there could be a popular new format. Haven't heard of one since Illumina switched gears a year or so ago. Anyway, you were asking about other tools. I am partial to trimmomatic myself.

      Comment


      • #4
        Originally posted by fznajar View Post
        It seems the new fastQ files have slightly different format that fastx quality filter tool cannot recognize it. Is there anything else out there?
        Thanks
        There is an option to specify the correct quality score.

        I've found fastx to be really slow, so I have switched to Trimmomatic.
        --------------
        Ethan

        Comment

        Latest Articles

        Collapse

        • 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
        • seqadmin
          Multiomics Techniques Advancing Disease Research
          by seqadmin


          New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

          A major leap in the field has
          ...
          02-08-2024, 06:33 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 02-28-2024, 06:12 AM
        0 responses
        21 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-23-2024, 04:11 PM
        0 responses
        69 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-21-2024, 08:52 AM
        0 responses
        77 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-20-2024, 08:57 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X