fixed QA_Illumina_report.rb encoding

[biopieces.git] / bp_scripts / QA_Illumina_report.rb

diff --git a/bp_scripts/QA_Illumina_report.rb b/bp_scripts/QA_Illumina_report.rb
index d50238509b04e6e47900762cb9fa3d387a91cc8d..6e0ba0a4c10c9ec695daf0c81dd1fb0c5f591c6c 100755 (executable)
--- a/bp_scripts/QA_Illumina_report.rb
+++ b/bp_scripts/QA_Illumina_report.rb
@@ -66,11 +66,11 @@ 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 -l 6 -L 6 -f ACACGACGCTCTTCCGATCT -r AGATCGGAAGAGCACACGTC |
    clip_adaptor |