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Old 05-20-2010, 09:24 AM   #1
kakar_nipun
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Default using bfast for mapping bacterial and viral genomes

Hi All

I was intending to map SOLID reads to the viral and bacterial genomes, and was thinking if i can use the same indices as mentioned in the Bfast manual, or do i need to create new ones?

After reading under advanced topics in the manual, i felt that using the same indices might just be stringent. Can someone throw some more light on this?
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Old 05-20-2010, 11:37 AM   #2
nilshomer
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Quote:
Originally Posted by kakar_nipun View Post
Hi All

I was intending to map SOLID reads to the viral and bacterial genomes, and was thinking if i can use the same indices as mentioned in the Bfast manual, or do i need to create new ones?

After reading under advanced topics in the manual, i felt that using the same indices might just be stringent. Can someone throw some more light on this?
They should work well for the viral and bacterial genomes.
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Old 05-20-2010, 12:14 PM   #3
drio
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Quote:
Originally Posted by kakar_nipun View Post
Hi All

I was intending to map SOLID reads to the viral and bacterial genomes, and was thinking if i can use the same indices as mentioned in the Bfast manual, or do i need to create new ones?

After reading under advanced topics in the manual, i felt that using the same indices might just be stringent. Can someone throw some more light on this?
There has been a lot of work behind the default indexes used for human (check support material from the paper). There is also code butil/btestindexes that
can help you test how they behave with different error rates, indels, etc... I would strongly suggest to create your own indexes (and compare with the default ones).
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