pid=$$
progress_meter |
-plot_lendist -t post -o 00_remove_adaptor_lendist_seq_before.$pid.ps -k SEQ_LEN |
find_adaptor -a $adaptor -p |
-plot_histogram -t post -o 01_remove_adaptor_histogram_adaptor_pos.$pid.ps -k ADAPTOR_POS -s num |
-plot_lendist -t post -o 02_remove_adaptor_lendist_adaptor_len.$pid.ps -k ADAPTOR_LEN |
-plot_lendist -t post -o 03_remove_adaptor_lendist_seq_after.$pid.ps -k SEQ_LEN |
-analyze_vals -k ADAPTOR_POS,ADAPTOR_LEN -o 04_remove_adaptor_analyze_vals.$pid.txt |
+plot_histogram -t post -o 00_remove_adaptor_histogram_adaptor_pos.$pid.ps -k ADAPTOR_POS -s num |
+plot_lendist -t post -o 01_remove_adaptor_lendist_adaptor_len.$pid.ps -k ADAPTOR_LEN |
+analyze_vals -k ADAPTOR_POS,ADAPTOR_LEN -o 02_remove_adaptor_analyze_vals.$pid.txt |
clip_adaptor |
-plot_scores -t post -o 04_trim_seq_scores_pretrim.$pid.ps |
-plot_lendist -k SEQ_LEN -t post -o 05_trim_seq_lendist_pretrim.$pid.ps |
+plot_scores -t post -o 03_trim_seq_scores_pretrim.$pid.ps |
+plot_lendist -k SEQ_LEN -t post -o 04_trim_seq_lendist_pretrim.$pid.ps |
trim_seq |
grab -e "SEQ_LEN>=30" |
mean_scores -l |
grab -e "SCORES_LOCAL_MEAN>=15" |
-plot_scores -t post -o 06_trim_seq_scores_posttrim.$pid.ps |
-plot_lendist -k SEQ_LEN -t post -o 07_trim_seq_lendist_posttrim.$pid.ps
+plot_scores -t post -o 05_trim_seq_scores_posttrim.$pid.ps |
+plot_lendist -k SEQ_LEN -t post -o 06_trim_seq_lendist_posttrim.$pid.ps