How to extract unmapped reads to assemble a plasmid

Question

[Barbara]

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.

Answer 1

[Trivas]

If you get a bam file or sam file, you can use samtools view, see How To Filter Mapped Reads With Samtools

[Barbara]

Hi again. I recovered unmapped reads using Snippy, but I am obtaining unmapped_R1, unmapped_R2, but also unmapped R0 and SE. Is it possible to perform an assembly usign these 4 files (I was planning to use unicycler or spades). Tks!