Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Generate consensus sequence with Samtools mpileup?

    Hey all,

    I have been unable to do this. When running the two lines of code shown here at the top (http://samtools.sourceforge.net/mpileup.shtml) it states that -u is an illegal option. This is with version 1.18. Has anybody else experienced this or do any of you have a way to generate the consensus sequence?

  • #2
    Nevermind, we got it to work with this:

    ./samtools mpileup -uf /<reference_seq.fa> <aligned_file.bam> | /samtools-0.1.18/bcftools/bcftools view -bcg - > <intermediate.bcf>

    /samtools-0.1.18/bcftools/bcftools view <intermediate.bcf> > output.txt

    Comment


    • #3
      Consensus Making

      This is great! It solved the problem I've been having with a bit of resequencing. Do you know of any way to turn this into fasta format, or is there a better execution of this?

      I'm trying to use this to close some mispairings in my genome, using Bowtie, followed by this. It's removed all of my "N's", but now I need to write it out to fasta.

      Thanks

      Comment


      • #4
        See previous thread http://seqanswers.com/forums/showthread.php?t=11536

        Comment


        • #5
          I've just gotten the hang of the Tuxedo pipeline, but I'm new to samtools. Right now I have a bunch of genes that were unnamed according to my annotation, but I can view the reads and their consensus for each transcript in samtools tview, after getting the genome coordinates from cummeRbund. Does anyone know of a way I can give samtools a genomic coordinate from cummeRbund and so it will give me a consensus sequence for all the reads that map to that section, even if there are multiple exons? Thanks.

          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
          9 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