added nucleotide plot to QA_454_report

[biopieces.git] / bp_scripts / QA_454_report.sh

diff --git a/bp_scripts/QA_454_report.sh b/bp_scripts/QA_454_report.sh
index 33f0a426341b85f04bcbd54f29299491c5aa335d..99f89e8290a247c779d71469b7c2fcb9f7ec66d2 100755 (executable)
--- a/bp_scripts/QA_454_report.sh
+++ b/bp_scripts/QA_454_report.sh
@@ -115,12 +115,14 @@ for sff_file in $sff_files; do
     echo "" && echo "Locating and counting MID tags ... "
     read_fastq -i $fq_file |
     progress_meter |
+    clip_seq |
     find_mids |
     write_tab -o $table_mid -c -k MID_NUM,MID_SEQ,MID_COUNT -x
 
     echo "" && echo "Locating and counting MID tags for sequences longer than 250 ... "
     read_fastq -i $fq_file |
     progress_meter |
+    clip_seq |
     grab -e 'SEQ_LEN >= 250' |
     find_mids |
     write_tab -o $table_mid_len -c -k MID_NUM,MID_SEQ,MID_COUNT -x
@@ -128,6 +130,7 @@ for sff_file in $sff_files; do
     echo "" && echo "Locating and counting MID tags for sequences longer than 250 and mean score above 20 ... "
     read_fastq -i $fq_file |
     progress_meter |
+    clip_seq |
     grab -e 'SEQ_LEN >= 250' |
     mean_scores |
     grab -e 'SCORES_MEAN >= 20' |