bowtie 2 alignment error

Question

[Msadeghibiology91]

Iinsert this command: bowtie -t -p 8 -n 1 -e 1 --best --sam -un DRR022467.unaligned.fastq mm9 DRR022467.fastq DRR022467.sam and got it:

-u/--qupto arg must be at least 1

what is it mean?

Answer 1

[Santosh Anand]

It should be --un instead of -un in your command line. In case of doubt, always refer to the manual for help http://bowtie-bio.sourceforge.net/manual.shtml