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  • Bowie outputs very few alignments

    Hi,

    I am trying to map my contigs, in fasta format, assembled using velvet from a 454 single read data. After the assembly i tried to reconfirm the assembly by mapping it with reference genome.

    I selected a reference genome based on 16S phylogenetic analysis, very close relative and I was expecting a good mapping of reference with my assembled contigs.

    Unfortunately I received only 0.07% alignment results which was shoking. I cross checked the mapping with SOAP and it also gave me not very different 0.9% overall alignment.

    Does it mean I have errors in assembly? Since I am sure that the mapping results can not be 0.07%. OR 16S based comparison is not a good criteria to select reference genomes??

    any ideas guyzz??

  • #2
    Bowie outputs very few alignments

    Use blast to align your contigs to the reference genome of a related species.

    Use bowtie or another aligner to align your 454 reads to the velvet contigs.

    It's also quite possible that velvet doesn't do a great job on 454 reads.

    Comment


    • #3
      Originally posted by mastal View Post
      Use blast to align your contigs to the reference genome of a related species.

      Use bowtie or another aligner to align your 454 reads to the velvet contigs.

      It's also quite possible that velvet doesn't do a great job on 454 reads.
      Hi Mastal.

      Thanks for your replies. I will try to do what you have suggested.

      Comment

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