Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • How to use Novoalign Paired End mode in command line?

    Topic.

    The documentation appears to be too confusing. All I need to know is how to enter my input in the command line so I can get the output.

  • #2
    Did you go through the quick start tutorial? The examples there are short.

    Comment


    • #3
      Ya, but the syntax is too confusing. I'm simply just trying to take my pair-end reads and align them to the reference genome.

      I have mastered it in BWA already, but I was told to try novoalign. In BWA, I only had to enter in 3 options essentially, pair1, pair2, and the ref.

      Comment


      • #4
        Well, it's not really that different for simple cases:
        Code:
        novoalign -d index -o SAM -f read1 read2
        I guess you don't really need "-o SAM", but the output won't be as useful otherwise.

        Edit: I should mention that "index" is just a placeholder for whatever you called the index/database/whatever-novoindex-calls-it and read1/read2 are the fastq files for reads 1 and 2, respectively.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • 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

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X