This is my data: http://www.ncbi.nlm.nih.gov/sra?term=SRP003871

AFTER removing the adapter and the read with Ns, the length of left reads is 18-40bp

Now I want map the reads to ref genome (to find piRNA (24-32bp)), I tried this:

bin/pass -d genome.fa -seeds_step 3 -fastq reads.fastq -check_block 500000 -Ns_percent -p 11111111 -sensitivety 3 fle 18 -l -cpu 12 -flc 1 -fid 90 -phred64 -b -sam -seq_gff > result.gff

but it does not work. I do not know how to adjust the parameters.

The experiment aimed extracting reads with 18-36 bp-->sequencing--->then finding out the piRNA(24-32bp)

Software: http://pass.cribi.unipd.it/cgi-bin/pass.pl