BBMerge saving unmerged reads

Question

[from the mountains]

Is there any way to save the unmerged reads to separate files when using bbmerge?

I am attempting to merge reads with overlap using bbmerge, but would also like to save unmerged reads, preferably separately to R1 and R2 files.

Answer 1

[finswimmer]

Hello,

bbmerge has the paramater outu for this. For example:

bbmerge in1=read1.fastq.gz in2=read2.fastq.gz out=merged.fastq.gz outu1=read1.unmerged.fastq.gz outu2=read2.unmerged.fastq.gz

fin swimmer