Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Is specifyng -Q33 in fastx_clipper for Sanger/Illumina1.9 encoding fastq important?

    Hi,

    I have fastq files which as Sanger/Illumina1.9 encoding. When I clipped off the linkers I havent specified the -Q33 but still it trimmed the linkers. As I didnt mention the Q33 parameter, is my fastq files fit for further mapping?

    Thanks in advance

  • #2
    Q33 is a measure of sequencing quality. You can get more information from THIS LINK

    You must get rid off of sequences that are badly sequenced because it will give you problems

    Comment


    • #3
      Originally posted by AntonioRFranco View Post
      Q33 is a measure of sequencing quality. You can get more information from THIS LINK

      You must get rid off of sequences that are badly sequenced because it will give you problems
      Thanks for your comment. In that case I think I should use -Q33 parameter whevener I Clipp or trimm the sequence using fastx right? Kindly guide me

      Comment


      • #4
        You must decide what value use to trim your sequences for quality
        A filter of Q33 is pretty high. If you use that value, you will discard many useful sequences

        Where is the border?

        SOme users do a filtering of Q20, other Q25. Sometimes a compromise is required.

        Use FastQC to get an idea of how many sequences you discard after filtering. FAstQC provides you with that information, and the graphics you get, are coloured with give you some simple explanation or valoration. Sometimes you simply make the sequences shorter, by discarding those sequences at the edge that are badly sequenced..

        Look for tutorials about FastQC. You will find it very easy to use

        Comment


        • #5
          All Illumina data (of recent vintage) uses Phred+33 offset (Sanger fastq format). If your data is in that format then you should specify -Q33 when using fastx. This option was not documented for fastx toolkit (it still may not be) and results in this oft asked question.

          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