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??
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??
Comment