I want to use Bowtie to align reads on a genome in order to look for miRNA.
I'm encountering troubles with running it.
Here is my command line
bowtie -q -S -a -l 18 -n 0 -e 80 -m 5 --best --strata /data/Genomes/mm9/bowtie1/mm9 ../cutadapt/mirCE1.cut.fastq mirCE1_bowtie.sam -al reads_alignes_genome.fa
When I run it, I got the following message:
-l/--seedlen arg must be at least 5
Does someone know what is the problem with my command line?
Thanks a lot.