Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • fastq to fasta conversion

    How can I convert my fastq files to two fasta files with one containing the reads and another containing the quality scores?

    Thanks

  • #2
    You could use awk to create a simple fasta file from your fastq, e.g.

    awk 'NR % 4 == 1 {print ">" $0 } NR % 4 == 2 {print $0}' my.fastq > my.fasta

    However, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences.

    Comment


    • #3
      Originally posted by Bio.X2Y View Post
      However, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences.
      ... and their corresponding qualities ..

      mySeq.fasta :
      >mySeq
      ACGTACGT

      mySeq.fasta.qual:
      >mySeq
      22 22 33 33 22 22 33 44

      There are still some programs which need to be fed with fasta/qual :-)

      Anyway, qualities need to be converted to phred-stye ..

      Comment


      • #4
        Thanks sklages! I wasn't aware of qual files.

        kwtennis311, there seem to be some existing posts on this, you might find answers in this, e.g. http://seqanswers.com/forums/showthread.php?t=3730.

        Comment


        • #5
          thanks

          thanks guys, Biopython did the trick

          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
          33 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-08-2024, 08:03 AM
          0 responses
          72 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