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  • help on a simple (?) assembly task

    Hi,

    I've never done an actual assembly before so I'm hoping someone can give me some advice to a presumably simple task.

    I've got some 100base read paired end genome sequence data of an organism where the genome sequence is not known. At the moment, I have a gene of interest in a closely related organism, and all I want to do is use this gene of interest sequence as a template to:

    1.Pull out closely matching reads from my data using Bowtie
    2.Use those reads to create a scaffold using velvet (?)
    3. Use this initial scaffold to then just extend a couple of kb on either side, again with velvet (?)

    Basically, I just want to deduce the orthologue with 5',3' UTR from the dataset.

    Is my workflow correct?
    Should I be using other software?
    Can velvet be set to limit assembly to within a defined range from an initial contig/scaffold?

    Thanks for any advice.

  • #2
    anyone have any sort of advice?
    thanks.

    Comment


    • #3
      An alternative approach could be to assemble all of your reads first, and then on the contig-level search for (e.g. by BLAST) sequences similar to your gene of interest.

      Comment


      • #4
        thanks for the reply.

        That was my first thought but unfortunately I am limited in computing power (6cpus and only 4 gigs of RAM) at the moment and thus need kind of a clumsy way of doing it.

        I've actually managed to use bowtie to identify reads aligning to this reference, and then input these into velvet to produce a couple of contigs.

        What I'd like to do is now use these contigs as an anchor to just extend out the assembly for a couple of kb's, but I can't figure out an option to do this in velvet, or if I should take a different approach now.

        Any more suggestions?
        cheers

        Comment

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