Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Pseudo-molecule

    Hi,

    How may I concatenate contigs into a single pseudo-molecule using a linker sequence? Does anyone know of a script for this purpose?

  • #2
    Well if you don't care about contig ordering then just put a bunch of 'N's (I suggest 100) between each contig. I'd probably use 'sed' for this. Something like:

    sed -e 's/>.*/NNNNNNNNNNNNNNNNNN/' <input.fasta>output.fasta

    Then reformat if desired (I used fasta_formatter) and put a header on top of the combined sequence.

    Comment


    • #3
      I'm not really sure i understand what you are asking for or why.

      but here is my take;

      cat contigs.fa | perl -p -e 's/^>.*/LINKER/g' | perl -p -e 's/\n//g' > Pseudo.fa

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Quality Control Essentials for Next-Generation Sequencing Workflows
        by seqadmin




        Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

        Nucleic Acid Quality Control
        Preparing for NGS starts with isolating the...
        02-10-2025, 01:58 PM
      • seqadmin
        An Introduction to the Technologies Transforming Precision Medicine
        by seqadmin


        In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
        01-27-2025, 07:46 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 02-07-2025, 09:30 AM
      0 responses
      68 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-05-2025, 10:34 AM
      0 responses
      108 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-03-2025, 09:07 AM
      0 responses
      83 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 01-31-2025, 08:31 AM
      0 responses
      47 views
      0 likes
      Last Post seqadmin  
      Working...
      X