adaptor script posilished

[biopieces.git] / bp_scripts / remove_adaptor.sh

diff --git a/bp_scripts/remove_adaptor.sh b/bp_scripts/remove_adaptor.sh
index daf036b82a76769592312482e84edcb180fff1d4..c5181c8cf6ada1093c712b90af7ba7bf8b62fb28 100755 (executable)
--- a/bp_scripts/remove_adaptor.sh
+++ b/bp_scripts/remove_adaptor.sh
@@ -4,10 +4,11 @@
 
 # Usage: read_fastq -i test.fq | remove_adaptor.sh | write_fastq -xo test_no_adaptor.fq
 
-adaptor='AGATCGGAAGACACACGTCT'  # Solexa adaptor
-#adaptor='TCGTATGCCGTCTTCTGCTTG' # 454 adaptor
+#adaptor='AGATCGGAAGACACACGTCT'  # Solexa adaptor
+adaptor='TCGTATGCCGTCTTCTGCTTG' # 454 adaptor
 pid=$$
 
+#find_adaptor -a $adaptor |
 parallel -k --blocksize 50M --pipe --recend "\n---\n" "nice -n 19 find_adaptor -a $adaptor" |
 plot_histogram -t post -o remove_adaptor_histogram.$pid.ps -k ADAPTOR_POS -s num |
 plot_lendist -t post -o remove_adaptor_lendist.$pid.ps -k ADAPTOR_LEN |