Entering edit mode
4.5 years 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.
Does this size and GC% represent chromosome and plasmid parts combined? If so, how do I separate chromosome information and plasmid information?
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.
How many contigs are there and have you tried to blast some of the smaller ones to see if they hit a plasmid?