Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how do i find a specific sequence in a bam file?

    I want to extract special sequences out of my bam-file (reference-mapped with BWA).

    normally i do that with blast or blat, but this time i have a bam file, not a ready-to-use genome...
    do i have to assemble the mapped reads into a consensus sequence in bevore, or is it possible to first (1.) identify the respective scaffold via the reference-genome with blat, (2.) assemble the reads that mapped to this scaffold and then (3.) aligne my sequence to that assembled scaffold?Or is this idea totally stupid? :/

    I have never done an assembly so far. Iam really unsure what is the right way here...

    Which tool would you suggest for assembling a bam-file, when dealing with genomes of >2 GB? And how shoud I care fore heterozygous positions?


    so many thanks in advance,
    hope anyone can give me here some help

  • #2
    It is hard for me to understand what you need. It appears that you already have reference-mapped data thus denovo assembly does not seem to required. If instead you are asking either (a) how to extract reads of a certain region or (b) how to call SNPs/Indels then you should look at the samtools 'mpileup' command. See http://samtools.sourceforge.net/mpileup.shtml for a starting place on mpileup.

    Comment


    • #3
      Have you tried to convert your BAM file into a SAM or Fasta?

      Use in the command line:

      $ samtools view -h -o out.sam in.bam
      The SAM file will provide the mapped reads into a specific scaffold. There you can retrieve your reads. Then you can assemble the reads

      Comment


      • #4
        first of all, thanks for answering!

        sorry for my imprecise question.

        What i have done so far is a reference-mapping of 5 genomes. i used BWA for that. everything worked well.

        Now i want to have the sequence of ~25 genes outof these 5 inidividuals. And i am not really sure how to do it.
        I have no experience how much time it takes to assemble the reads of these 5 individuals to a consesus sequence... therefore i thougth: maybe it is enought to just assemble the parts of the individuals in which the genes are lying...

        @amarth: which program do you suggest for the assembly. And how should i care for heterozygous sites? Shoud I use ambiguity code in the final gene sequence, or "Ns"?

        Thanks!

        Comment

        Latest Articles

        Collapse

        • seqadmin
          The Impact of AI in Genomic Medicine
          by seqadmin



          Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
          02-26-2024, 02:07 PM
        • seqadmin
          Multiomics Techniques Advancing Disease Research
          by seqadmin


          New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

          A major leap in the field has
          ...
          02-08-2024, 06:33 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 02-28-2024, 06:12 AM
        0 responses
        21 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-23-2024, 04:11 PM
        0 responses
        69 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-21-2024, 08:52 AM
        0 responses
        77 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-20-2024, 08:57 AM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X