Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Novoalign Output Missing

    Hi,
    I have run novoalign in multiple ways, but each time when the program finishes running, I cannot find the output file! -o just specifies the output format. There are no errors during the run. Can you tell me where the alignment file is or how I could find it?
    Thank you!

  • #2
    ./novoalign -o SAM -d [file.novoindex] -f [read_1] [read_3] 1> [output.sam] 2> [output.metrics]

    That should be a basic way to run it.

    Comment


    • #3
      That worked perfectly. THANK YOU!!

      Comment


      • #4
        Hi guys!

        Just resurrecting this thread - had exactly the same problem as the OP, but now it works.

        Just what exactly are the output.metrics?

        Comment


        • #5
          Like the number of reads, number of aligned etc.

          Originally posted by TabeaK View Post
          Hi guys!

          Just resurrecting this thread - had exactly the same problem as the OP, but now it works.

          Just what exactly are the output.metrics?

          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, 07-16-2024, 05:49 AM
          0 responses
          24 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-15-2024, 06:53 AM
          0 responses
          31 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-10-2024, 07:30 AM
          0 responses
          40 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-03-2024, 09:45 AM
          0 responses
          205 views
          0 likes
          Last Post seqadmin  
          Working...
          X