From 6420a0576fd75c449289ea86fc429e9d9fb836c4 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Tue, 10 May 2011 16:49:36 +0000 Subject: [PATCH 1/1] fixed pipes for adaptor removal git-svn-id: http://biopieces.googlecode.com/svn/trunk@1398 74ccb610-7750-0410-82ae-013aeee3265d --- bp_scripts/remove_adaptor_454.sh | 17 +++++++++++++++++ ...ve_adaptor.sh => remove_adaptor_illumina.sh} | 0 2 files changed, 17 insertions(+) create mode 100755 bp_scripts/remove_adaptor_454.sh rename bp_scripts/{remove_adaptor.sh => remove_adaptor_illumina.sh} (100%) diff --git a/bp_scripts/remove_adaptor_454.sh b/bp_scripts/remove_adaptor_454.sh new file mode 100755 index 0000000..34013b1 --- /dev/null +++ b/bp_scripts/remove_adaptor_454.sh @@ -0,0 +1,17 @@ +#!/bin/sh + +# Remove adaptor from sequences and produce a number of plots. + +# Usage: read_fastq -i test.fq | remove_adaptor.sh | write_fastq -xo test_no_adaptor.fq + +adaptor='TCGTATGCCGTCTTCTGCTTG' # 454 adaptor +pid=$$ + +#find_adaptor -a $adaptor | +plot_lendist -t post -o 00_remove_adaptor_lendist_seq_before.$pid.ps -k SEQ_LEN | +parallel -k --blocksize 50M --pipe --recend "\n---\n" "nice -n 19 find_adaptor -a $adaptor" | +plot_histogram -t post -o 01_remove_adaptor_histogram_adaptor_pos.$pid.ps -k ADAPTOR_POS -s num | +plot_lendist -t post -o 02_remove_adaptor_lendist_adaptor_len.$pid.ps -k ADAPTOR_LEN | +plot_lendist -t post -o 03_remove_adaptor_lendist_seq_after.$pid.ps -k SEQ_LEN | +analyze_vals -k ADAPTOR_POS,ADAPTOR_LEN -o 04_remove_adaptor_analyze_vals.$pid.txt | +clip_adaptor diff --git a/bp_scripts/remove_adaptor.sh b/bp_scripts/remove_adaptor_illumina.sh similarity index 100% rename from bp_scripts/remove_adaptor.sh rename to bp_scripts/remove_adaptor_illumina.sh -- 2.39.2