楼主跑以下程序时分别弹出了“fastq_quality_filter: Invalid quality score value (char ‘.‘ ord 46 quality value -18) on line 12”和“fastq_quality_filter: Invalid quality score value (char ‘#‘ ord 35 quality value -29) on line 4”的错误提示
fastq_quality_filter -q 20 -p 70 -i ERR499.unknowNul1.fastq -o ERR499.qual1.fastq fastq_quality_filter -q 20 -p 70 -i ERR499.unknowNul2.fastq -o ERR499.qual2.fastq
解决此类错误需要在命令行添加“-Q33”的参数，修改为以下命令，即可去除低质量reads：
fastq_quality_filter -q 20 -p 70 -Q33 -i ERR499.unknowNul1.fastq -o ERR499.qual1.fastq fastq_quality_filter -q 20 -p 70 -Q33 -i ERR499.unknowNul2.fastq -o ERR499.qual2.fastq
原文：http://www.cnblogs.com/chenwenyan/p/6269796.html