STDERR.puts "Analyzing sequences ... "
system(
- "read_fastq -i #{seq_file} |
+ "read_fastq -e illumina1.8 -i #{seq_file} |
progress_meter |
analyze_vals -k SEQ -o #{analyze_vals_file} |
trim_seq -l 3 -m 25 |
- grab -e 'SEQ_LEN > 0' |
+ grab -e 'SEQ_LEN > 20' |
analyze_vals -k SEQ -o #{analyze_vals_trim_file} |
find_adaptor -l 6 -L 6 -f ACACGACGCTCTTCCGATCT -r AGATCGGAAGAGCACACGTC |
clip_adaptor |