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Expand title How many contigs were generated in each case? 2 for the plasmid and 16 for the full
Code Block language bash title Where does the answer come from? collapse true grep -c "^>" unmapped*/contigs.fasta
Expand title Are any of the contigs the same? Yes, both contigs detected in the plasmid mode were also detected in the full mode
Code Block language bash title Where does the answer come from? collapse true grep "^>" unmapped*/contigs.fasta # lists identical lengths and coverages for 2 plasmid contig
Expand title What sizes are the contigs? 5441
3170
14 others less than 500bp
Code Block language bash title Where does the answer come from? collapse true grep "^>" unmapped*/contigs.fasta # same command as above, just focusing on the length value
Expand title which is most likely to be our plasmid? The contig that is 3170.
Code Block language bash title Where does the answer come from? collapse true # From above, I stated this was a high copy plasmid, it has a coverage value of 12,698 compared to 98 for the larger contig
Expand title Is that actually our plasmid? Yes! The actual plasmid reference locus line stats:
LOCUS GFP_Plasmid_Sequ 3115 bp DNA circular UNA 18-NOV-2013
Expand title Why might the sizes not agree? My thought is that this was raw fastq files that were fed into the assembly, not trimmed files. Leads me to hypothesize that the difference in size is related to the presence of adapter sequence.
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