I am running Bowtie2 to get mapped reads as well as unmapped reads. The following command gives mapped reads:
bowtie2 -x rRNA -U file.fq -S file.sam
And the below command gives unmapped reads:
bowtie2 -x rRNA -U file.fq --un file_filtered.fq
How to run one command to get both mapped and unmapped reads? THANK YOU!