Determine if the reads in a .fasta file of a bacteria contains plasmid
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21 months ago
suzuBell ▴ 60

I have the reads in a .fasta file for a bacterial strain. I was able to assemble these reads into contigs and determine the size (bp) and GC% of all this information.

  1. Does this size and GC% represent chromosome and plasmid parts combined? If so, how do I separate chromosome information and plasmid information?

  2. I would like to determine whether or not this .fasta file contains plasmid(s), or if it is entirely chromosome data. If plamids are present, I would like to know the number and each of their size (bp) and GC%. How can this be achieved?

Thank you for any guidance you may provide.

plasmid chromosome bacteria • 485 views
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How many contigs are there and have you tried to blast some of the smaller ones to see if they hit a plasmid?

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