Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bowtie output and reference genome question

    Hello, a quick question for anybody familiar with bowtie. In my reference genome files, which have names like SVID_XXX, the first line of text, before the actual sequence data is a line like >Chromosome, or >ContigXXXX, .... In the bowtie output data, Chromosome or ContigXXXX shows up as the file name it mapped to instead of SVID_XXX, the actual file name. My question is this, is bowtie taking the > symbol in the first line of text as a command to redirect to this file name or whatever comes after it in that line? I know that > redirects output to a file, but why does this happen in bowtie since the file already has a file name, and > only shows up in the first line of a text file? I hope this makes sense, any thoughts?

  • #2
    Your reference genome files are FASTA files.

    The FASTA file format is simple.
    There is one line, starting with the symbol ">" which describes the sequence.
    The first word after ">" is the name of the sequence.
    Following the sequence description is the sequence itself.

    Bowtie and all programs dealing with raw genomic data are written to be able to parse FASTA files.

    The FASTA format has nothing to do with the Unix redirection operator, and dates back to 1985.
    Last edited by blancha; 11-13-2015, 07:50 PM.

    Comment


    • #3
      Thanks, that helps a lot.

      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
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 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