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Old 05-04-2013, 05:37 AM   #1
kumarS_27
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Location: Italy

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Default 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??
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Old 05-04-2013, 06:13 AM   #2
mastal
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Default 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.
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Old 05-04-2013, 07:50 AM   #3
kumarS_27
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Default

Quote:
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.
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