plasmid spades R1/R2 files?
Hello,
I know spades innately saves the corrected R1/R2 fastq files for the assembly. However, the plasmid spades program only uses a subset of those reads, so I was wondering if there is a flag or way to pull out just those reads used to build the plasmid assembly and place them in separate R1/R2 files?
I am also open to using other mapping methods (BWA) but I just don't know how to split fastq files into genomic and plasmid DNA.
Thanks!
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sarah.goldstein •
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If you have the genomic reference available you can use an aligner (look into
bbmap.shfrom BBMap suite withoutu=file.fq.gzoption) to collect reads that do not map. Those should be your plasmid reads (assuming there is no other entity expected to be present).