Bowie outputs very few alignments

[kumarS_27]

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??

[mastal]

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.

[kumarS_27]

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.