Ion torrent Bam to Annotation
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6.1 years ago
alok.helix ▴ 80

I sequenced a bacterial genome using Ion Torrent machine and I assembled the reads against a reference genome (closely related to the sequenced Bacteria). Now I have the bam file. I plan on using Prokka to annotate my data. I believe Prokka doesnot take in a bam file for annotation purpose. What should i do further? Should i extract a consensus sequence from the bam file?? If so How should i proceed and if wrong, how will i proceed?? Also how to get gene infromation into the vcf file??

 

https://github.com/tseemann/prokka/blob/master/README.md#invoking-prokka

genome Assembly SNP alignment sequencing • 1.7k views
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