How to extract unmapped reads to assemble a plasmid
Hi all, I have illumina reads for an E coli J53 and its transconjugant, it is an E coli J53 that received a plasmid. I would like to map the reads of the transconjugant to the E coli J53 assembly and keep the unmapped reads, to use them to perform a new assembly and construct the plasmid that was transferred during conjugation.
I was planning to use BWA-MEM, in order to filter out the chromosomal DNA. But I do not have idea how to recover the unmapped reads.
I would appreciate your help.
1 answer
If you get a bam file or sam file, you can use samtools view, see How To Filter Mapped Reads With Samtools
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