I have chip-seq reads of bad quality (dm3) - 29,772,199 reads:
Tried to trim it with fastq_quality_filter (command line fastq_quality_filter -q 20 -p 100 -i infile.fastq -o outfile.fastq) and got only 410,775 reads:
Is that OK? Otherwise, what should I do to these data? I suppose I should't just push it to bowtie for alignment..