Entering edit mode
9.4 years ago
biolab
★
1.4k
Hi, everyone,
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!
In both yours and mine it'll have both mapped and unmapped alignments. If you just want the mapped alignments in it then
bowtie2 --no-unal --un file_filtered.fq -x rRNA -U file.fq -S file.sam
should work.Hi Devon, Thanks a lot!