From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 26 Apr 2011 10:22:31 +0000 (+0000)
Subject: adaptor script posilished
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=0c0f1dec090a43200896d006f4d23c50d3c3216a;p=biopieces.git

adaptor script posilished

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1348 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_scripts/remove_adaptor.sh b/bp_scripts/remove_adaptor.sh
index daf036b..c5181c8 100755
--- 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 |