3 # Remove adaptor from sequences and trim according to scores.
4 # Produces a number of plots during the process.
6 # Usage: read_fastq -i test.fq | clean_reads.sh | write_fastq -xo clean.fq
8 #adaptor='TCGTATGCCGTCTTCTGCTTG' # 454 adaptor
9 adaptor='AGATCGGAAGACACACGTCT' # Solexa adaptor
13 find_adaptor -a $adaptor -p |
14 plot_histogram -t post -o 00_remove_adaptor_histogram_adaptor_pos.$pid.ps -k ADAPTOR_POS -s num |
15 plot_lendist -t post -o 01_remove_adaptor_lendist_adaptor_len.$pid.ps -k ADAPTOR_LEN |
16 analyze_vals -k ADAPTOR_POS,ADAPTOR_LEN -o 02_remove_adaptor_analyze_vals.$pid.txt |
18 plot_scores -t post -o 03_trim_seq_scores_pretrim.$pid.ps |
19 plot_lendist -k SEQ_LEN -t post -o 04_trim_seq_lendist_pretrim.$pid.ps |
21 grab -e "SEQ_LEN>=30" |
23 grab -e "SCORES_LOCAL_MEAN>=15" |
24 plot_scores -t post -o 05_trim_seq_scores_posttrim.$pid.ps |
25 plot_lendist -k SEQ_LEN -t post -o 06_trim_seq_lendist_posttrim.$pid.ps