Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • in silico restriction digest of Illumina reads (fastq file)

    Hi

    I wonder whether anyone has a solution for a restriction digestion script that works on fastq files (Illumina reads), splitting any reads that contain the restriction site into two separate reads (and writing it back into the fastq file)?

    Actually I am not so much interested in restriction as such - I have reads from co-ligated and nebulized PCR fragments, so I'd like to separate those reads at the ligation junctions, and I thought I could tweak a restriction script (preferentially, Perl) into doing that.

    Any hints appreciated.

    regards,
    Berthold

  • #2
    Hi Berthold,

    Did you ever find a solution to doing in silico digestion of fastq files and writing output back into fastq format files? I've been trying to do this with the Bio.Restriction module of BioPython, but the output is fasta (with read quality data being lost).

    Regards,
    Gareth

    Comment


    • #3
      Thanks for the hint Gareth.
      No I did not find a way to do it otherwise yet (but it wasn't high priority). There's a student in my group now who is good with Python, I'll consult with him.

      best regards,
      Berthold

      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