Hello,
I'm interested in determining if plasmid sequences are in a NGS data set and I was thinking about creating a master fasta file with the sequences for each plasmid and then aligning NGS data to that master file and determining 1) if the sample has a plasmid and 2) which one(s).
My questions are 1) Does it make sense to use one fasta file containing all the plasmid sequences
>plasmid 1
ATGC
>plasmid 2
AGCT
>Plasmid 3
ATGTT
or should I have one fasta file for each plasmid?
2) What software could I use to visualize which plasmid has reads mapping to it? If multiple plasmids are mapped to, etc.?
Thank you
I'm interested in determining if plasmid sequences are in a NGS data set and I was thinking about creating a master fasta file with the sequences for each plasmid and then aligning NGS data to that master file and determining 1) if the sample has a plasmid and 2) which one(s).
My questions are 1) Does it make sense to use one fasta file containing all the plasmid sequences
>plasmid 1
ATGC
>plasmid 2
AGCT
>Plasmid 3
ATGTT
or should I have one fasta file for each plasmid?
2) What software could I use to visualize which plasmid has reads mapping to it? If multiple plasmids are mapped to, etc.?
Thank you
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