Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • PatrickReed
    Junior Member
    • Oct 2011
    • 2

    Super Large Reference Genome

    I am working on a project in which i am analyzing RNAseq data from fused interspecific cell types, specifically mouse cells and rat cells, and then performing. Being confident that a given read came from the mouse genome or the rat genome is crucial thus the optimal reference genome would be the union of mm9.fa and rn4.fa, but the size is too large for build with bowtie/tophat. Is their anyway to build this reference genome? Why is there a set limit on the size that a reference genome can be. Any help would be greatly appreciated. I know there are work arounds by performing alignemnts to one genome then the other and looking at differences and overlap so on and so forth but this is not optimal.

    Cheers,
  • maubp
    Peter (Biopython etc)
    • Jul 2009
    • 1544

    #2
    Are you trying to use a single concatenated sequence? Is so, why not use a multi-entry FASTA file containing both the rat and the mouse chromosomes?

    The SAM/BAM format itself has a limit of 2^31 - 1 base pairs for each reference sequence, or about 2Gbp (2 billion base pairs). In theory this could be raised to 2^32 - 1 or about 4Gbp but it would cause trouble for Java tools. However, you are much more likely to hit a limitation in the current BAM indexing scheme (BAI files) of 512Mbp (or half a billion base pairs), which is a problem for some organisms - but not for mice, rats or humans!

    Perhaps there is some other limiting factor in bowtie/tophat as well?

    Comment

    • ffinkernagel
      Senior Member
      • Oct 2009
      • 110

      #3
      Yes, bowtie indices use 32 unsigned integers which limits them to about 4gb.
      Going up to 64 bit integers would double the memory requirement and probably also slow down the alignment process.

      You could extend bowtie to allow larger genomes - the SeqAn library it uses should even make this a pretty straightforward endeavour. Better ask the authors how to go about it though.

      Comment

      • PatrickReed
        Junior Member
        • Oct 2011
        • 2

        #4
        Thanks ffinkernagel, thats really helpful, i'll start looking at the SeqAn library and try to get in contact with the authors.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Pathogen Surveillance with Advanced Genomic Tools
          by seqadmin




          The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
          03-24-2025, 11:48 AM
        • seqadmin
          New Genomics Tools and Methods Shared at AGBT 2025
          by seqadmin


          This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

          The Headliner
          The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
          03-03-2025, 01:39 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-20-2025, 05:03 AM
        0 responses
        49 views
        0 reactions
        Last Post seqadmin  
        Started by seqadmin, 03-19-2025, 07:27 AM
        0 responses
        57 views
        0 reactions
        Last Post seqadmin  
        Started by seqadmin, 03-18-2025, 12:50 PM
        0 responses
        50 views
        0 reactions
        Last Post seqadmin  
        Started by seqadmin, 03-03-2025, 01:15 PM
        0 responses
        201 views
        0 reactions
        Last Post seqadmin  
        Working...