Print (un)classified sequences

[namnh7]

Hi there,

Could anyone tell me how to print unclassified/classified sequences in fastq (or fastq.gz) format. My input are paired-end reads in file_1/2.fq.gz.

Thanks for helping!

[rwhetten]

The --un-conc <path> option is supposed to "write pairs that didn't align concordantly to the designated path. If -gz or -bz2 is appended, e.g. --un-conc-gz <path>, output will be written in the corresponding compressed format.