X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_scripts%2FQA_Illumina_report.rb;h=6e0ba0a4c10c9ec695daf0c81dd1fb0c5f591c6c;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=f5b426f0a5e0987b6e73f860f176de2bdfef4212;hpb=1445a21d5065ea544c88be1103976c3feb63dca7;p=biopieces.git

diff --git a/bp_scripts/QA_Illumina_report.rb b/bp_scripts/QA_Illumina_report.rb
index f5b426f..6e0ba0a 100755
--- a/bp_scripts/QA_Illumina_report.rb
+++ b/bp_scripts/QA_Illumina_report.rb
@@ -66,13 +66,13 @@ scores_bin_file                = File.join(tmpdir, 'scores_bin.png')
 STDERR.puts "Analyzing sequences ... "
 
 system(
-  "read_fastq -i #{seq_file} |
+  "read_fastq -e base_33 -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 -c 12 -l 6 -L 6 -f ACACGACGCTCTTCCGATCT -r AGATCGGAAGAGCACACGTC |
+   find_adaptor -l 6 -L 6 -f ACACGACGCTCTTCCGATCT -r AGATCGGAAGAGCACACGTC |
    clip_adaptor |
    grab -e 'SEQ_LEN > 0' |
    analyze_vals -k SEQ -o #{analyze_vals_trim_noadapt_file} |