Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to use bambus for scaffolding?

    How to make mates file from the velvet contig output for bambus. The IID of velvet contig file(convert by amos package) is always the numbers, how can we tell the paired-end sequence from this file?

    Thanks!

  • #2
    Originally posted by elisadouzi View Post
    How to make mates file from the velvet contig output for bambus. The IID of velvet contig file(convert by amos package) is always the numbers, how can we tell the paired-end sequence from this file?

    Thanks!
    Hi,
    I am also trying to do the same. Have you already generated the bambus2 required input files(.contig and .mate)? I have .contig file from the minimus2 run, But I am not sure how to get .mate file. Can I generate it from the Illumina paired-end reads information? the reads I assembled??
    Best regards,
    Rahul
    Rahul Sharma,
    Ph.D
    Frankfurt am Main, Germany

    Comment


    • #3
      I gave up on bambus after wrestling with the docs for months. The paper makes it sound great, but I couldn't get it working.
      Homepage: Dan Bolser
      MetaBase the database of biological databases.

      Comment


      • #4
        Same here!
        Bambus2 within AMOS did not work for me either. Is it possible to open an a thread in this forum?

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Exploring the Dynamics of the Tumor Microenvironment
          by seqadmin




          The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
          07-08-2024, 03:19 PM
        • seqadmin
          Exploring Human Diversity Through Large-Scale Omics
          by seqadmin


          In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
          06-25-2024, 06:43 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Today, 11:09 AM
        0 responses
        15 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-19-2024, 07:20 AM
        0 responses
        147 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-16-2024, 05:49 AM
        0 responses
        121 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-15-2024, 06:53 AM
        0 responses
        111 views
        0 likes
        Last Post seqadmin  
        Working...
        X