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Forum: Bioinformatics 05-20-2010, 09:24 AM
Replies: 2
Views: 1,623
Posted By kakar_nipun
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?
Forum: Bioinformatics 03-01-2010, 10:33 AM
Replies: 1
Views: 2,352
Posted By kakar_nipun
Bfast query


I was trying to create indices for the reference genome using bfast 0.6.3.c and also trying to convert the reads.

Convert the reference:
bfast-0.6.3c/bfast/bfast fasta2brg -f microbial.fa
Forum: Bioinformatics 12-18-2009, 08:07 AM
Replies: 2
Views: 4,126
Posted By kakar_nipun
Calling indels from samtools-pileup

Hi Guys

I was not clear on the samtools indel calling documentation, and therefore wanted to clarify a few things. I observe the following cases in my samtools-indel calling output.
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